The BLAST search page enables you to interrogate the EST database for sequences similar to a sequence of your own using the BLAST programs. Paste your protein or nucleotide sequence , which can be either in plain text or FASTA format, into the first text box. You can decide whether to compare your sequence to the whole database or just ESTs from one organism. If you want to search the database with more than one sequence, do each search separately, rather than inputting them as a single FASTA file. Matches are only returned with an E-value less than the value in the Maximum E-value text box. Values can be entered in this box in either decimal or scientific notation i.e. 0.0001 or 1e-4 or 1E-4. You can also specify the maximum number of one line descriptions and alignments the BLAST program will output.
There are three BLAST programs which can be used to compare your sequence with the database sequences. If your sequence is a protein sequence, use the tblastn algorithm, which compares your protein sequence with EST sequences translated in all six possible reading frames. If your sequence is a nucleotide sequence you can either use blastn, which directly compares your nucleotide sequence with the EST sequences, or tblastx which compares the six-frame translations of your sequence against the six-frame translations of the EST sequences.The low complexity filter can be turned on or off, by default it is on which is suitable for most searches. Click on the Search button to BLAST search the database or the Reset button to clear the form. The full BLAST output is shown. You can get details on the unisequences by clicking on their names.