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Items tagged with "nucleotide" (17)
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Created: 05/03/08 @ 14:15:35 | Last updated: 31/03/08 @ 15:55:09
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves nucleotide and protein sequences with the literature and references associated
to them given a protein and a nucleotide id.
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Created: 13/01/10 @ 18:42:35 | Last updated: 17/11/10 @ 13:46:04
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow retrieves Liliopsida chloroplast petb gene sequences from NCBI Nucleotide, removes duplicate sequences and saves the results at BioExtract Server. These results are then converted into GenBank format and fed into Fetch Translation, which removes the translation from the CDS coding region. Translations are then used to build a multiple alignment using ClustalW.
Rating: 4.0 / 5 (1 rating) | Versions: 6 | Reviews: 0 | Comments: 3 | Citations: 1 Viewed: 544 times | Downloaded: 106 times Tags (5): |
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Created: 13/01/10 @ 18:47:06 | Last updated: 17/11/10 @ 13:57:19
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Bootstrapped sequences algorithm reads in a data set, and produces multiple data sets from it by bootstrap resampling. http://pro.genomics.purdue.edu/cgi-bin/emboss/help/fseqboot
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Created: 05/04/10 @ 06:13:16 | Last updated: 05/04/10 @ 06:13:17
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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.
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Created: 09/07/09 @ 21:39:54 | Last updated: 22/11/10 @ 23:16:42
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene
Rating: 5.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 152 times | Downloaded: 107 times Tags (8): |
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Created: 08/07/09 @ 16:26:13 | Last updated: 14/12/09 @ 11:59:14
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License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.
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Created: 19/03/10 @ 15:17:53
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Retrieves the genome seqn for both the target and source strains using gi nos
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Created: 21/07/10 @ 13:56:08 | Last updated: 21/07/10 @ 13:58:41
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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
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Original Uploader |
Created: 21/07/10 @ 14:08:32 | Last updated: 07/09/10 @ 10:04:55
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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
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Original Uploader |
Created: 21/07/10 @ 14:21:50 | Last updated: 21/07/10 @ 14:21:52
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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
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Original Uploader |
Created: 21/07/10 @ 14:36:36 | Last updated: 01/09/10 @ 17:35:20
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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
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Original Uploader |
Created: 17/06/10 @ 16:34:50 | Last updated: 19/07/10 @ 20:00:00
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow, created using the BioExtract Server, contains a nucleotide query (using the NCBI Core Nucleotide Database), Blastn (against the Homo sapiens genome), Blastn (against the Mus musculus genome), the Format Conversion tool, the Fetch Translator Tool, and ClustalW. This workflow was created following the analytical steps described in the journal article "Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced the...
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Original Uploader |
Created: 01/09/10 @ 17:26:07 | Last updated: 01/09/10 @ 17:26:39
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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
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Original Uploader |
Created: 01/09/10 @ 17:31:29 | Last updated: 01/09/10 @ 17:33:51
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Attributions:
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): |
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Created: 07/08/09 @ 16:04:23 | Last updated: 07/08/09 @ 16:23:53
A tutorial to demonstrate how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.
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Created: 07/08/09 @ 16:20:06 | Last updated: 07/08/09 @ 16:25:46
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This tutorial demonstrates how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.
File type: Word 2007 document Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 29 times | Downloaded: 25 times Tags: |
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Created: 17/03/11 @ 11:21:06 | Last updated: 17/03/11 @ 11:21:12
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of all the SNP found with the Villard et al., (2002) QTL for Bilateral Perisylvian Polymicrogyria.
Please download this data as you wish, and use in whatever study you like. The data is open access, and freely available for all to use to help undertand this condition.
Genes related to these SNP can be found in the file http://www.myexperiment.org/files/466.
File type: ZIP archive Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 10 times | Downloaded: 6 times Tags: |
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