institute for computational biomedicine: seqinfo

[ description ]

Seqinfo is a utility which can be used to rapidly summarise output from the BLAST suite of programs. It is generally used to find the most similar matches for genes or proteins of unknown identity.

[ about the method ]

Link to Crover documentation page

[ documentation ]

The version of crover which includes this utility currently installed on our system is crover_release_wmc1.0. There are a number of different ways of using this tool. The tool can take either a FASTA sequence file, a Blast output file in XML format, or a MegaBLAST output file in -D3 format. The following examples illustrate the different usages. Before running any of these examples, set your CROVER environmental variable to the latest release version (e.g., /usr/global/opt/any/pkg/crover).

FASTA sequence file example

XML BLAST output file example

MegaBLAST output file example

The manual for seqinfo is available below:

seqinfo manual

An explanation of the output file format is given below:

output format

[ availability ]

seqinfois available on all machines [ access seqinfo]

News

Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

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Events

Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301