Gramene User Help

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BLAST

Is there a tutorial or help section on how to use BLAST?

Yes. Please refer to the BLAST tutorials, help files and release notes at http://www.gramene.org/tutorials/BLAST.html.

What are some examples of scientific queries that can be answered using BLAST?

You can search for the pairwise sequence match to your query sequence. The pairwise match can lead to a region of the rice genome, or help you find a match to an EST or a contig of ESTs, CDSs, or a protein or rice gene homolog.

Which BLAST programs are available?

Gramene BlastView provides access to the following algorithms: BLASTN for simple nucleotide against nucleotide searches BLASTP for simple protein versus protein searches TBLASTN for a protein query versus a DNA library search BLASTX for DNA query versus protein library TBLASTX for a translated DNA query against a translated DNA database The interface will guide the user choosing the correct algorithm for the given search problem. Depending on query and subject library sequences, not all of the algorithms will thus be available.

Against which sequence databases can I do a BLAST query?

Available databases include assembled genomic sequence, gene model cDNAs and Peptides, ESTs, EST clusters, BACends, GSS reads, GSS clusters and marker sequences. In general, each database corresponds to an individual genome browser track. The collection of databases grows with each Gramene release.

Is my BLAST query configurable?

BlastView provides two levels of configuration. Firstly, one can select the sensitivity to optimise certain types of searches - exact matches through to distant hologies. Secondly, one can use the 'CONFIG' page for fine-grained control over individual blast parameters.

I have submitted a BLAST job, why does my browser hang?

Your BLAST request will run immediately and return results directly to your web browser in HTML format. In certain cases, BLAST searches can take a long time to complete, sometimes so long that the web browser times out. You can take the following steps to increase the speed of the BLAST: - Ensure that the sensitivity option is set as low as possible - Use BLASTN rather than TBLASTX (which can take 9 times longer) - Split long query sequences into smaller chunks - Repeatmask the query sequence before submission

Can I search with multiple query sequences?

Yes, you can enter up to 10 sequences at a time.

Why do some alignments report "No data" in the "Chromosome" column of the results page?

Many entries in the sequence databases have no significant alignment with the genome. Matches against these cannot, therefore, be projected into genomic coordinates.

I use TblastX to search for homology of my sequences. How can I determine the minimum score to consider as significant for classification?

You can use the 'configure' option of the BlastView interface to set the tblastx parameters to any that you want. We cannot suggest any minimum score as such, as this will depend on many factors specific to your sequences. A good reference on the subject is Korf et.al.'s O'Reilly book on Blast - www.oreilly.com/catalog/blast/

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