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[ synopsis ]

tisearch
-seqs | -xml filename [-tiac filename] [-dna/-protein] [-db database] [-e E-value] [-b number_alignments] [-v number_descriptions] [-minimumLength length] [-percentIdentity percent_identity]

[ description ]

Searches a database using BLAST using the specified parameters (i.e. -db, -e, -b, -v), determines which matches fulfil the specified criteria (i.e. -minimumLength, -percentIdentity) and outputs the resulting matches to the tiac output file, in XML format.

[ options ]

-seqs | -xml
Sequence input filename
The FASTA sequence input file, which will be used as the BLAST query.
Default value: none

-tiac
Output filename
Creates the output file. If the filename does not end with .tiac, this suffix will automatically be appended.
Default value: tiac

-dna / -protein

Determines whether the query sequences in the input file are DNA or protein, which determines which BLAST program is to be used.
Default value: protein

-db
Database
Sets the database to be searched by BLAST.
Default value: est

-e
Expectation value (double)
Sets the expectation value to be used as a cut-off in the BLAST search.
Default value: 1e-20

-b
(Integer)
Sets the number of alignments to be returned by BLAST. The higher the number, the more potential matches.
Default value: 1000000

-v
(Integer)
Sets the number of descriptions returned in the BLAST output. This should be the same as the number of alignments returned (cf -b) because both alignments and descriptions are used to determine which matches satisfy the criteria given by -minimumLength and -percentIdentity.
Default value: 1000000

-minimumLength
Minimum length (integer)
Sets the minimum length that the HSP between the query sequence and the subject sequence must span for a match to be considered. The default value of 50 is recommended for protein sequences; 150 recommended for DNA sequences.
Default value: 50

-percentIdentity
Percent identity (double)
Sets the minimum percent identity that the HSP between query and subject sequence must satisfy for match to be considered.
Default value: 0.95 (i.e. 95% sequence identity)

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