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CRT home > TissueInfo: mRNAs Tutorial

To predict the tissue distribution of a set of mRNAs, follow these steps:

Obtain a FASTA file with the query sequences of the mRNAs. Use the mrnas.fasta file as an example. Make sure mrnas.fasta provides a unique accession code for each mRNA. (The accession code is used to analyse the results.)

Search dbEST for ESTs that match the query sequences. As query sequences are nucleotide sequences, and because we interested in very good matches, we can use MegaBLAST: megablast -i mrnas.fasta -d est -e 1e-20 -D 3 >mrnas.mbout

Convert mrnas.mbout to a tiac file. The conversion removes hits that MegaBLAST identified but are not exact matches and should not be used for tissue expression profile prediction. The -assemble-hsps tag is used to accumulate the length of all HSPs from the same query sequence (which pass the sequence identity threshold). timegablast --mb mrnas.mbout --tiac mrnas.tiac --db est --evalue 1e-20 --assemble-hsps

Query the mrnas.tiac file for tissue information. The following command requests a few calculations to be performed for each query sequence found in the tiac file. tiquery -tiac mrnas.tiac -out mrnas -mostExpressedIn \ -report -numPlant \ -tissueSummary

Check out the results. The last step should have created three files: mrnas.data, mrnas.schema, mrnas.report.

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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