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Items tagged with "sequence" (54)

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Workflows (52)

Taverna 1 Original Uploader Duncan Hull	Genome annotation pipeline demonstrator workflow for Nucleic Acids Research (v2) Created: 03/10/07 @ 18:35:47 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Part of a workflow by Hannah Tipney, adapted by Duncan Hull using GenScan, RepeatMasker and BLAST. http://dx.doi.org/10.1093/nar/gkl320 Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 549 times \| Downloaded: 162 times Tags (5): bioinformatics \| segregation \| sequence \| sequence assembly \| sequence tagged site	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	BLAST using DDBJ service (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 03/12/09 @ 16:31:20 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP... Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 579 times \| Downloaded: 213 times Tags (5): bioinformatics \| BLAST \| ddbj \| sequence \| similarity	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	BLASTP with simplified results returned (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 03/12/09 @ 16:28:50 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV... Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 323 times \| Downloaded: 106 times Tags (6): bioinformatics \| BLAST \| ddbj \| sequence \| similarity \| simplifier	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Simplify a BLAST text file (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 28/07/09 @ 13:01:45 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc. Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 357 times \| Downloaded: 140 times Tags (11): bioinformatics \| BLAST \| gene identifier \| gi \| matrix \| sequence \| similarity \| simple \| simplifier \| substitution \| summary	View Download (v2)
Taverna 1 Original Uploader Kieren Lythgow	Multiple Blastp (v2) Created: 20/11/07 @ 16:58:38 \| Last updated: 10/01/08 @ 12:09:38 Credits: Kieren Lythgow License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a workflow to automate multiple BLASTp jobs on a large list of protein sequences in FASTA format. Rating: 5.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 482 times \| Downloaded: 157 times Tags (4): bioinformatics \| BLAST \| protein \| sequence	View Download (v2)
Taverna 1 Original Uploader M.B.Mon...	Workflow for Protein Sequence Analysis (v1) Created: 09/01/08 @ 12:03:03 \| Last updated: 09/01/08 @ 12:31:27 Credits: M.B.Monteiro Attributions: BLAST using DDBJ service Simplify a BLAST text file conditional branch License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis. Rating: 4.0 / 5 (2 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1615 times \| Downloaded: 430 times Tags (10): analysis \| BLAST \| homology \| multiple sequence alignment \| phylogenetic tree \| protein \| sequence \| tree \| wpsa	View Download (v1)
Taverna 1 Original Uploader Alan Williams	Retrieve sequence in EMBL format (v3) Created: 17/06/09 @ 16:51:32 Credits: Franck Tanoh Tomoinn Stuart Owen License: Creative Commons Attribution 3.0 Unported License This workflow retrieves a sequence associated with its features in embl format Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 307 times \| Downloaded: 100 times Tags (8): bioinformatics \| example \| mygrid \| rendering \| retrieval \| sequence \| soaplab \| taverna	View Download (v3)
Taverna 1 Original Uploader Franck Tanoh	BLASTP with simplified results returned (v2) Created: 03/10/07 @ 18:36:12 \| Last updated: 06/03/08 @ 17:01:32 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow Performs a blastp search on protein sequence, extracts sequence id within the blast report and retrives the corresponding seuqences. Rating: 4.0 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 192 times \| Downloaded: 58 times Tags (3): bioinformatics \| BLAST \| sequence	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Retrieve Protein Sequence (v1) Created: 30/07/08 @ 16:36:55 \| Last updated: 03/12/09 @ 16:54:02 Credits: Katy Wolstencroft License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 384 times \| Downloaded: 128 times Tags (5): bioinformatics \| neuroscience \| newcastle \| protein \| sequence	View Download (v1)
GWorkflowDL Original Uploader Andreas Hoheisel	Workflow Pattern - Sequence (v1) Created: 03/12/08 @ 14:17:20 Credits: Andreas Hoheisel License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow is a GWorkflowDL representation of a sequence that sequentially invokes A and B. This workflow is equivalent to the following pseudo code: end_A = A(); end_B = B(end_A); Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 54 times \| Downloaded: 31 times Tags (6): d-grid \| example \| gwes \| gworkflowdl \| sequence \| workflow pattern	View Download (v1)
Taverna 1 Original Uploader Kieren Lythgow	Biomart Protein Sequence Retrieval (v1) Created: 09/03/09 @ 11:38:10 Credits: Kieren Lythgow License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 179 times \| Downloaded: 46 times Tags (5): biomart \| ensembl \| FASTA \| protein \| sequence	View Download (v1)
Taverna 1 Original Uploader Andrea Wiggins	DOI Record Generator (v1) Created: 29/04/09 @ 16:39:57 Credits: Andrea Wiggins Attributions: Data Set Metadata Generator License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow generates DOI record files for deposit, using data set metadata for the FLOSSmole project. It reads in an input file generated from a SQL query from an eprints database, and transforms the parts of the source file as necessary to create a comprehensive DOI deposit record. It also generates DOIs for the data sets. These metadata are inserted into an XML record template (based on the std-doi.xsd schema) and the individual resources are aggregated into a single file. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 107 times \| Downloaded: 32 times Tags (7): data management \| doi \| metadata \| repository \| sequence \| text \| xml	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Using CQL to query protein sequence data (v1) Created: 07/05/09 @ 14:28:59 Credits: Stian Soiland-Reyes Attributions: Using CQL to query protein sequence data License: Creative Commons Attribution-Share Alike 3.0 Unported License To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 155 times \| Downloaded: 69 times Tags (10): cabig \| cabio \| cagrid \| cancer research \| cpas \| globus \| grid service \| gridpir \| protein \| sequence	View Download (v1)
Taverna 2 Original Uploader cory (Kazuki Oshita)	G-language Genome Analysis Environment - GC skew analysis (basic) (v2) Created: 05/04/10 @ 06:20:58 Credits: cory (Kazuki Oshita) License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow calculates and graphs the GC skew of a given genome sequence. Use this as a template for using more than 100 analysis programs implemented in G-language Genome Analysis Environment, which can be used in a similar manner. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 40 times \| Downloaded: 19 times Tags (5): analysis \| g-language \| genome \| sequence \| workflow	View Download (v2)
Taverna 2 Original Uploader cory (Kazuki Oshita)	G-language Genome Analysis Environment - GC skew analysis (sequence retrieval via togoWS) (v2) Created: 05/04/10 @ 06:24:02 Credits: cory (Kazuki Oshita) License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow calculates and graphs the GC skew (by default, for keto bases, with window size of 1000) of a given genome sequence identifier. Here the genome sequence in Fasta format is downloaded through the Togo Web Service with RefSeq identifier. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 47 times \| Downloaded: 35 times Tags (5): analysis \| g-language \| genome \| sequence \| workflow	View Download (v2)
Taverna 2 Original Uploader cory (Kazuki Oshita)	G-language Genome Analysis Environment - Basic sequence manipulations (v2) Created: 05/04/10 @ 06:13:16 \| Last updated: 05/04/10 @ 06:13:17 Credits: cory (Kazuki Oshita) License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow shows simple sequence manipulation functions of G-language GAE, such as random shuffling, obtaining a reverse complement, and translation of nucleotide sequences, and showing basic composition statistics for nucleotide and amino acid sequences. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 23 times \| Downloaded: 18 times Tags (5): g-language \| nucleotide \| sequence \| translation \| workflow	View Download (v2)
Taverna 2 Original Uploader cory (Kazuki Oshita)	G-language Genome Analysis Environment - GC skew analysis (multiple) (v2) Created: 05/04/10 @ 06:22:28 Credits: cory (Kazuki Oshita) License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow calculates and graphs the GC skew of a given genome sequence (for the entire genome, for only the coding sequences, for only the intergenic regions, and for only the third codon positions), as well as the GC content with sliding windows. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 29 times \| Downloaded: 25 times Tags (5): analysis \| g-language \| genome \| sequence \| workflow	View Download (v2)
Taverna 2 Original Uploader cory (Kazuki Oshita)	G-language Genome Analysis Environment - GC skew analysis (AT skew) (v3) Created: 05/04/10 @ 06:17:25 \| Last updated: 09/01/11 @ 06:08:19 Credits: cory (Kazuki Oshita) License: GNU General Public License (GPL) 2.0 This workflow calculates and graphs the AT skew of a given genome sequence, using options of gcskew program. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment. Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 32 times \| Downloaded: 21 times Tags (5): analysis \| g-language \| genome \| sequence \| workflow	View Download (v3)
Taverna 2 Original Uploader Stian Soiland-Reyes	EBI_InterProScan for Taverna 2 (v2) Created: 26/01/10 @ 14:46:07 \| Last updated: 26/01/10 @ 14:46:08 Credits: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam Attributions: EBI InterproScan T2 EBI_InterProScan License: Creative Commons Attribution-Share Alike 3.0 Unported License Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 175 times \| Downloaded: 122 times Tags (5): interpro \| interproscan \| looping \| sequence \| term	View Download (v2)
Taverna 2 Original Uploader Stian Soiland-Reyes	EBI_InterProScan for Taverna 2 (v2) Created: 26/01/10 @ 14:45:46 \| Last updated: 24/11/10 @ 10:04:09 Credits: Stian Soiland-Reyes Katy Wolstencroft Paolo Hamish McWilliam Attributions: EBI_InterProScan for Taverna 2 EBI InterproScan T2 EBI_InterProScan EBI InterProScan License: Creative Commons Attribution-Share Alike 3.0 Unported License Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to t... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 394 times \| Downloaded: 197 times Tags (6): interpro \| interproscan \| looping \| sequence \| term	View Download (v2)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and EMBOSS analysis (v1) Created: 03/07/09 @ 14:18:28 \| Last updated: 03/07/09 @ 14:19:32 Credits: Stian Soiland-Reyes Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 3.0 Unported License Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 86 times \| Downloaded: 23 times Tags (6): alignment \| analysis \| sequence \| services \| soaplab \| workflow	View Download (v1)
Taverna 1 Original Uploader Angela Luijf	DNA sequence analysis pilot (v1) Created: 10/07/09 @ 14:31:27 \| Last updated: 30/11/09 @ 09:37:38 Credits: Angela Luijf Glatard License: Creative Commons Attribution-No Derivative Works 3.0 Unported License http://amc-app1.amc.sara.nl/twiki/bin/view/ Workflow-based DNA sequence analysis on the Dutch Life Science Grid, presented as Application Showcase at the NBIC Conference 2009, Lunteren, The Netherlands, 17 & 18 March 2009. http://www.biomedgrid.it/programme may 15th 2009. Hands on workflow: grid-enabled medical imaging (Johan Montagnat – Tristan Glatard) Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 335 times \| Downloaded: 46 times Tags (5): grid \| moteur \| sequence \| taverna 1 \| workflow	View Download (v1)
Taverna 1 Original Uploader Angela Luijf	DNA sequence analysis pilot (Blat) (v2) Created: 20/11/09 @ 11:12:43 \| Last updated: 30/11/09 @ 09:35:38 Credits: Angela Luijf Barbera van Schaik Glatard Attributions: DNA sequence analysis pilot License: Creative Commons Attribution-Share Alike 3.0 Unported License http://amc-app1.amc.sara.nl/twiki/bin/view/ Workflow-based DNA sequence analysis on the Dutch Life Science Grid. This workflow is based on http://www.myexperiment.org/workflows/840 , the last component (Blast analysis) is replaced by Blat analysis Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 84 times \| Downloaded: 22 times Tags (7): analysis \| DNA \| grid \| moteur \| sequence \| taverna 1 \| workflow	View Download (v2)
Taverna 2 Original Uploader Ian Laycock	Compare genome, extract proteins which are drug targets, apply to KEGG pathway (v1) Created: 19/03/10 @ 13:16:24 \| Last updated: 19/03/10 @ 13:33:53 Credits: Ian Laycock nclteamc Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects License: Creative Commons Attribution-Share Alike 3.0 Unported License Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga... Rating: 4.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 150 times \| Downloaded: 58 times Tags (7): colour \| FASTA \| gi \| kegg \| pathway \| proteins \| sequence	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	Retrieve Genome Seqn using gi nos (v1) Created: 19/03/10 @ 15:17:53 Credits: Ian Laycock nclteamc License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieves the genome seqn for both the target and source strains using gi nos Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 10 times Tags (5): FASTA \| genome \| gi \| nucleotide \| sequence	View Download (v1)
Taverna 2 Original Uploader cory (Kazuki Oshita)	G-language Genome Analysis Environment - Bacteria Analysis System (v2) Created: 05/04/10 @ 06:08:25 \| Last updated: 05/04/10 @ 06:08:26 Credits: cory (Kazuki Oshita) License: GNU General Public License (GPL) 2.0 Given an identifier for genome sequence (by default, genome of Mycoplasma genitalium: refseq:NC_000908) or raw sequence data in FASTA format, this workflow calculates and graphs the following properties using the G-language Genome Analysis Environment: GC skew (gcskew), cumulative GC skew (gcskew_cumulative), GC skew of coding/intergenic/GC3 (genomicskew), GC content with sliding windows (gcwin), replication origin and terminus (find_ori_ter), codon usage table (codon_usage), the Codon Adapta... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 58 times \| Downloaded: 42 times Tags (5): FASTA \| g-language \| genome \| sequence \| workflow	View Download (v2)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:16:00 \| Last updated: 21/07/10 @ 13:23:12 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 13 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a BLAST with options from DDBJ Web services (v1) Created: 21/07/10 @ 13:24:56 \| Last updated: 01/09/10 @ 17:37:48 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html exxample accession : Q9NRA8 database : UNIPROT program : blastp param : -b 5 -m 7 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 11 times Tags (5): bioinformatics \| BLAST \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:56:08 \| Last updated: 21/07/10 @ 13:58:41 Credits: Lebreton Attributions: BLAST using DDBJ service License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example : accession : AB000100 database : DDBJ program : blastn Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 9 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a high speed BLAST and extract position from DDBJ Web services (v4) Created: 21/07/10 @ 14:08:32 \| Last updated: 07/09/10 @ 10:04:55 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7 Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 28 times \| Downloaded: 16 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v4)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a BLAST with options from DDBJ Web services (v1) Created: 21/07/10 @ 14:21:50 \| Last updated: 21/07/10 @ 14:21:52 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 10 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a VecScreen from DDBJ Web services (v1) Created: 21/07/10 @ 14:36:36 \| Last updated: 01/09/10 @ 17:35:20 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a VecScreen from DDBJ Web services : A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin informations on Web services available at http://xml.nig.ac.jp/index.html accession : AB000100 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 11 times Tags (4): bioinformatics \| nucleotide \| sequence \| services	View Download (v1)
Taverna 2 Original Uploader Bas Vroling	BLAST against the GPCRDB (v1) Created: 24/08/10 @ 13:45:14 \| Last updated: 24/08/10 @ 13:45:16 Credits: Bas Vroling License: Creative Commons Attribution-Share Alike 3.0 Unported License With this workflow you can submit a BLAST query to the GPCRDB. Input requires a sequence with amino acids only. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 37 times \| Downloaded: 22 times Tags (4): BLAST \| gpcrdb \| protein \| sequence	View Download (v1)
Taverna 2 Original Uploader Bas Vroling	Create custom-made GPCR alignments (v1) Created: 24/08/10 @ 13:58:32 \| Last updated: 24/08/10 @ 13:58:35 Credits: Bas Vroling License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow allows you to create your own GPCR alignments. The alignments are built from the residues that are annotated with the general residue numbers. Alignments are therefore not built using standard alignment algorithms but are created by selecting residues that are likely to share the same position in the three-dimensional structure. Users can select the proteins and residue positions that should be aligned, allowing for the creation of e.g. an alignment of all binding pocket residue... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 32 times \| Downloaded: 26 times Tags (5): alignment \| ballesteros-weinstein \| gpcrdb \| protein \| sequence	View Download (v1)
Taverna 1 Original Uploader Achille Zappa	M_Fetch_e-T_phylo_boot - (BETA) (v1) Created: 10/03/10 @ 15:44:02 \| Last updated: 10/03/10 @ 15:49:06 Credits: Achille Zappa Hamish McWilliam License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 13 times Tags (12): alignment \| analysis \| clustal \| consensus \| fetch \| ml \| muscle \| nj \| phylogeny \| protein \| sequence \| tree	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a high speed BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:16:24 \| Last updated: 01/09/10 @ 17:18:45 Credits: Lebreton Attributions: retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 13 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:22:14 \| Last updated: 01/09/10 @ 17:22:37 Credits: Lebreton Attributions: retrieve protein sequence and do a BLAST and extract position from DDBJ Web services License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 11 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a high speed BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:26:07 \| Last updated: 01/09/10 @ 17:26:39 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 6 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:31:29 \| Last updated: 01/09/10 @ 17:33:51 Credits: Lebreton Attributions: retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example : accession : AB000100 database : DDBJ program : blastn Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 8 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blast_ParseBlast (v1) Created: 22/09/10 @ 12:40:55 \| Last updated: 22/09/10 @ 13:35:26 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License Blast Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 15 times Tags (9): alignment \| BLAST \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blat (v1) Created: 22/09/10 @ 13:18:55 \| Last updated: 22/09/10 @ 13:35:49 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database http://www.bioinformaticslaboratory.nl/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 14 times Tags (9): alignment \| blat \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blast_Blat_ParseBlast (v1) Created: 22/09/10 @ 13:22:57 \| Last updated: 22/09/10 @ 13:36:12 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License Blast and Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 17 times Tags (10): alignment \| BLAST \| blat \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	EBI_NCBI_BLAST (v1) Created: 17/01/11 @ 12:51:58 \| Last updated: 17/01/11 @ 12:52:03 Credits: Katy Wolstencroft Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs an NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 34 times Tags (13): async \| asynchronous services \| BLAST \| blastp \| database \| ebi \| example \| looping \| ncbi \| ncbi blast \| protein sequence \| sequence \| uniprot	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	BiomartAndEMBOSSAnalysis (v4) Created: 27/01/11 @ 17:03:03 \| Last updated: 12/05/11 @ 13:31:41 Credits: Katy Wolstencroft Alan Williams Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 102 times \| Downloaded: 55 times Tags (16): alignment \| biomart \| biomart emboss \| bonn \| disease \| emboss \| emma \| ensembl \| gene \| genes \| homolog \| human \| mouse \| sequence \| sequence alignment \| soaplab	View Download (v4)
Taverna 2 Original Uploader Rafael C. Jimenez	DAS sequence retrieval (v2) Created: 30/05/11 @ 01:20:35 \| Last updated: 30/05/11 @ 01:26:47 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS). Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 6 times Tags (4): das \| genome \| protein \| sequence	View Download (v2)
Taverna 2 Original Uploader Rafael C. Jimenez	DAS sequence retrieval and parsing with JDAS (v1) Created: 30/05/11 @ 03:12:23 \| Last updated: 30/05/11 @ 03:14:03 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS, copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 6 times Tags (5): das \| genome \| jdas \| protein \| sequence	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	DAS features retrieval (v2) Created: 01/06/11 @ 17:10:43 \| Last updated: 01/06/11 @ 17:57:45 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS). Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 4 times Tags (3): annotation \| das \| sequence	View Download (v2)
BioExtract Server Original Uploader Carol Lushbough	tblastx non-redundant alignment (v1) Created: 30/06/11 @ 15:26:13 \| Last updated: 04/07/11 @ 16:51:41 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species. For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1. Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2. The output from ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 4 times Tags (7): alignment \| gene \| genomic \| proteins \| sequence \| species \| workflow	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	EBI NCBI BLAST Multi FASTA (v2) Created: 16/07/11 @ 19:08:38 \| Last updated: 16/07/11 @ 19:35:11 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 17 times Tags (6): BLAST \| ebi \| FASTA \| fasta format \| sequence \| similarity	View Download (v2)
Taverna 2 Original Uploader Bas Vroling	BLAST your sequences against the NucleaRDB (v1) Created: 19/08/11 @ 10:32:03 \| Last updated: 19/08/11 @ 10:41:38 Credits: Bas Vroling License: Creative Commons Attribution-Share Alike 3.0 Unported License BLAST your sequences against the NucleaRDB. Input requires a sequence with amino acids only (no fasta format etc) Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 5 times Tags (4): BLAST \| nucelardb \| protein \| sequence	View Download (v1)
Taverna 2 Original Uploader cory (Kazuki Oshita)	KEIO Bioinformatics Web Service - a generating sequence logo image for a set of sequence retrieval via homology search (v2) Created: 13/08/10 @ 14:02:59 \| Last updated: 19/11/10 @ 05:32:37 Credits: cory (Kazuki Oshita) License: GNU General Public License (GPL) 2.0 This workflow generates a sequence logo image for a set of amino acid sequences of FOXP2 gene, by downloading the amino acid sequences in Fasta format through Togo Web Service with UniProt identifiers (togoWS, provided by the G-language Genome Analysis Environment SOAP Service), running BLAST web service (runBLAST), retrieving a set of sequences from ID list (togoWS), aligning the sequence with MUSCLE (runMUSCLE), extracting a certain region from the alignment (extractalign, provided by Soapl... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 35 times \| Downloaded: 28 times Tags (9): BLAST \| FASTA \| g-language \| kbws \| muscle \| protein \| sequence \| togows \| weblogo	View Download (v2)
Taverna 2 Original Uploader Ankit upadhyay	(Updated)Retrieve sequence in EMBL format. (v1) Created: 19/03/12 @ 11:59:57 \| Last updated: 02/04/12 @ 22:51:40 Credits: Ankit upadhyay License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow retrieves a sequence associated with its features in embl format. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 1 \| Comments: 6 \| Citations: 0 Viewed: 9 times \| Downloaded: 5 times Tags (5): fcvbg \| fggtd \| gerger \| id \| sequence	View Download (v1)

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Paul Fisher

Next Generation Sequencing

Unique name: NextGenSeq Created: Monday 23 November 2009 @ 11:20:47 (GMT)

This group is for people wishing to contribute / find out more about 'Next Generation Sequencing' technology and data. Please feel free to join this group and add any workflows you think others may benefit from.

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Files (1)

Uploader:

Paul Fisher

Re-sequenced Daxx gene info

Created: 08/04/09 @ 17:53:46 | Last updated: 10/08/09 @ 12:30:59

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadsheet contains information about the re-sequencing of the daxx gene, identified as a candidate QTg for the African Trypanosomiasis resiatance phenotype. This file is related to the paper: http://www.ncbi.nlm.nih.gov/pubmed/17709344

File type: Excel workbook

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 29 times | Downloaded: 21 times

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