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Items tagged with "blastall" (6)

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Workflows (6)

Workflow EBI_NCBI_BLAST (1)

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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. Note: the WSNCBIBlast 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 NCBI BLA...

Created: 2008-05-31 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow EBI_NCBI_BLAST_with_prompts (1)

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Run a BLAST analysis using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be use...

Created: 2008-05-31 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

Workflow fetch_fasta (1)

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This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese...

Created: 2009-03-20 | Last updated: 2009-03-20

Credits: User Jumblejumble

Workflow blastp of target vs source database (1)

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This worlflow allows the user to input two sets of proteins in fasta format. One file is converted to a database using formatdb, the set is blasted against this database to test for Blast hits. Users is able to set eValue and destination of files for database and blast file. Arguments can be added to either formatdb or blast in beanshell supplied. Blast and formatdb must be installed locally and the correct filepaths for these applications must entered into the workflow accordingly.

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: User Ian Laycock Network-member nclteamc

Attributions: Workflow fetchEnsemblSeqsAndBlast

Workflow NCBI BLAST (SOAP) (1)

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

Created: 2010-11-29 | Last updated: 2013-03-28

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST Workflow NCBI BLAST (SOAP)

Workflow NCBI BLAST (SOAP) (1)

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

Created: 2010-11-29 | Last updated: 2013-03-28

Attributions: Workflow EBI_NCBI_BLAST Workflow NCBI BLAST (SOAP)

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Non-Information Resource URI: https://www.myexperiment.org/tags/825


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