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Creator:

Wassinki

Package: mapping oligonucleotides to an assembly

Created: 11/12/08 @ 12:02:48 | Last updated: 22/01/09 @ 09:06:27

5 items in this pack

Comments: 0 | Viewed: 108 times | Downloaded: 31 times

Original Uploader

Paul Fisher

BLAST using DDBJ service (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 03/12/09 @ 16:31:21

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: 0 | Citations: 0

Viewed: 367 times | Downloaded: 134 times

Original Uploader

Paul Fisher

Simplify a BLAST text file (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 28/07/09 @ 13:01:46

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: 243 times | Downloaded: 109 times

Original Uploader

M.B.Mon...

Workflow for Protein Sequence Analysis (v1)

Created: 09/01/08 @ 12:03:04 | Last updated: 09/01/08 @ 12:31:29

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: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 720 times | Downloaded: 243 times

Original Uploader

Hamish McWilliam

EBI_blastpgp_PSI-BLAST (v1)

Created: 31/05/08 @ 14:39:23

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Perform a PSI-BLAST iterative search using the EBI’s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 95 times | Downloaded: 43 times

Original Uploader

Hamish McWilliam

EBI_WU-BLAST (v1)

Created: 30/05/08 @ 22:47:19 | Last updated: 02/06/08 @ 21:30:18

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 163 times | Downloaded: 56 times

Original Uploader

Hamish McWilliam

EBI_NCBI_BLAST (v1)

Created: 31/05/08 @ 08:38:49 | Last updated: 02/06/08 @ 21:32:22

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 180 times | Downloaded: 95 times

Original Uploader

Katy Wolstencroft

Retrieve Protein Sequence and BLAST (v1)

Created: 09/11/07 @ 10:41:12 | Last updated: 05/06/08 @ 15:18:08

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves a protein sequence in Fasta format from Genbank and then performs a BLAST on that sequence

Rating: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 235 times | Downloaded: 12 times

Original Uploader

Hamish McWilliam

EBI_Blast2InterPro (v2)

Created: 07/06/08 @ 10:52:47 | Last updated: 26/10/08 @ 20:45:46

Credits: Hamish McWilliam

Attributions: EBI_WU-BLAST EBI_dbfetch_fetchBatch Fasta_string_to_fasta_list EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

Perform a BLAST search add information about the InterPro matches associated with the hits. This implementation uses: EBI’s WSWUBlast web service (http://www.ebi.ac.uk/Tools/webservices/services/wublast) to perform the initial BLAST search against UniProtKB. EBI’s WSDbfetch web service (http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) to retreive the sequences of the hits found by BLAST. 3. EBI’s WSInterProScan web service (http://www.ebi.ac.uk/Tools/webservices/services/interp...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 123 times | Downloaded: 52 times

Original Uploader

Wassinki

Blast against ENSEMBLE Danio_rerio_Genome (v1)

Created: 15/10/08 @ 08:43:51 | Last updated: 15/10/08 @ 09:21:36

Credits: Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to ins...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 59 times | Downloaded: 26 times

Original Uploader

Bas Vroling

blastp using the MRS system (v1)

Created: 28/11/08 @ 15:13:32 | Last updated: 28/11/08 @ 15:34:20

Credits: Bas Vroling

License: Creative Commons Attribution 3.0 Unported License

This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database name. Valid database names that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb". Output is returned in XML.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 63 times | Downloaded: 22 times

Original Uploader

Wassinki

Mapping OligoNucleotides to an assembly (v7)

Created: 11/12/08 @ 12:11:59 | Last updated: 13/02/09 @ 09:08:23

Credits: Wassinki Pieter Neerincx

Attributions: Blat against ENSEMBLE Danio_rerio_Genome BlatBlastCombi Blast against ENSEMBLE Danio_rerio_Genome AppendToFile Test Input for Mapping oligonucleotides to an assembly Input for Mapping oligonucleotides to an assembly

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 207 times | Downloaded: 41 times

Original Uploader

Carol Lushbough

Nucleotide InterProScan for the BioExtract Server (v3)

Created: 14/01/09 @ 16:53:47 | Last updated: 01/07/09 @ 08:32:35

Credits: Carol Lushbough Hamish McWilliam

Attributions: Nucleotide_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow can be downloaded and imported into the BioExtract Server at bioextract.org. This workflow is a BioExtract Server process similar to the Nucleotide InterProScan workflow designed and implement in Taverna by Hamish McWilliams. The InterProScan tool (http://www.ebi.ac.uk/Tools/InterProScan/) searches a protein sequence against a selection of protein domain, feature and family signature databases, and integrates the results giving potential assignments to InterPro entries and Gen...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 93 times | Downloaded: 69 times