Tag Results

Items tagged with "multiple sequence alignment" (16)

Note: some items may not be visible to you, due to viewing permissions.


Files (1)
Uploader

Blob BioExtract Server Workflow Tutorial

Created: 2009-08-07 16:20:06 | Last updated: 2009-08-07 16:25:46

Credits: User Carol Lushbough

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

Comments: 0 | Viewed: 58 times | Downloaded: 45 times

Tags:

Packs (1)
Creator

Pack BioExtract Server Workflow Tutorial


Created: 2009-08-07 16:04:23 | Last updated: 2009-08-07 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.

1 item in this pack

Comments: 0 | Viewed: 79 times | Downloaded: 23 times

Tags:

Workflows (14)

Workflow Workflow for Protein Sequence Analysis (1)

Thumb
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.

Created: 2008-01-09 | Last updated: 2008-01-09

Credits: User M.B.Monteiro

Attributions: Workflow BLAST using DDBJ service Workflow Simplify a BLAST text file Workflow conditional branch

Workflow EBI_ClustalW2 (2)

Thumb
Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSClustalW2 service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement ClustalW2 servi...

Created: 2009-04-07 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow EBI_ClustalW_alignment_tree (2)

Thumb
Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks.

Created: 2008-05-31 | Last updated: 2010-12-03

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree

Workflow Protein_search_fetch_align_tree (2)

Thumb
An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers...

Created: 2009-04-07

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree Workflow EBI_dbfetch_fetchBatch Workflow EBI_WU-BLAST

Workflow Protein_alignment_transmembrane (1)

Thumb
Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. Uses the EBI web services: WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/servic...

Created: 2008-06-01

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA Workflow EBI_ClustalW2 Workflow EBI_dbfetch_fetchBatch

Workflow EBI_Kalign (1)

Thumb
Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi...

Created: 2008-06-02 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow EBI_MAFFT (1)

Thumb
Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool. Note: the WSMafft service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MAFFT services (REST or SOAP) should be used instead.

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow EBI_MUSCLE (1)

Thumb
Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used. Note: the WSMuscle service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MUSCLE services (REST or SOAP) should be used instead.  

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow EBI_TCoffee (1)

Thumb
Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSTCoffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) is used. Note: the WSTCoffee service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement T-COFFEE services (REST or SOAP) should be used instead.  

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow Liliopsida Protein Alignment (6)

Thumb
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.

Created: 2010-01-13 | Last updated: 2010-11-17

Credits: User Carol Lushbough

Workflow EMBL-EBI ClustalW2 (SOAP) (1)

Thumb
Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).

Created: 2010-12-06 | Last updated: 2013-03-28

Attributions: Workflow EBI_ClustalW2

Workflow EMBL-EBI ClustalW2_SOAP (2)

Thumb
Perform a ClustalW2 alignment of protein sequences using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). This workflow 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.

Created: 2011-01-17 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EMBL-EBI ClustalW2 (SOAP) Workflow EBI_ClustalW2

Workflow NCBI Protein Clustal Omega Alignment (1)

Thumb
Searches NCBI Proteins for a given organism and protein. User VMatch (xmknr) Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks to remove possible dubplcate and clustal omega to generate a multiple sequence alignment. Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make u...

Created: 2012-08-31

Credits: User Carol Lushbough

Workflow Non-redundant protein alignments (1)

Thumb
Execute BLASTP program to search protein databases using a protein query: Input file from iPlant Discovery Environment Save the data extract of similar sequences created by BLASTP Execute XMKNR to a compute a non-redundant set from a large collection of protein sequences. Input from the data extract created by BLASTP. Perform multiple sequence alignments using Clustal Omega and TCoffee Input from data extract created by XMKNR To execute this workflow, you need to be logged into the Bio...

Created: 2012-12-19 | Last updated: 2012-12-19

Credits: User Carol Lushbough

What is this?

Linked Data

Non-Information Resource URI: https://www.myexperiment.org/tags/325


Alternative Formats

HTML
RDF
XML