What is BLAST?
Basic Local Alignment Search Tool. (Altschul et al.) A sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query. The initial search is done for a word of length "W" that scores at least "T" when compared to the query using a substitution matrix. Word hits are then extended in either direction in an attempt to generate an alignment with a score exceeding the threshold of "S". The "T" parameter dictates the speed and sensitivity of the search. For additional details, see one of the BLAST tutorials (Query or BLAST) or the narrative guide to BLAST.
INPUT SEQUENCE:
You can cut/copy and paste the nucleotide sequences or protein sequences in the sequence submission window. The sequences that you are submitting must be in FASTA format. [Sequences in FASTA formatted files are preceded by a line starting with a " >" symbol]. You are presently allowed to submit upto 15 sequences per run.
RESULTS:
Results of your analysis will be displayed in an easily interpretable table within your browser. You can also save the result table in PDF format.
PARAMETERS:
PROGRAM:
Choose here which of the BLAST search programs you want to use.
- BLASTP will compare a protein sequence against the protein database of your choice (see option DATABASE).
- BLASTX will translate a nucleic acid sequence in all six reading frames and compare all these against the protein database of your choice.
OPENGAP:
The gap open penalty is the score taken away for the initiation of the gap in sequence or in structure. To make the match more significant you can try to make the gap penalty larger. It will decrease the number of gaps and if you have good alignment without many gaps, its Z-score will be higher.
Default values:
- BLASTP: 11
- BLASTX: 11
- BLASTN: 5
Note: If you are looking for an open gap value that is not shown in the menu, change the extend gap, as a different range of open gap values will be displayed.
EXTENDGAP:
The gap extension penalty is added to the standard gap open penalty for each base or residue in the gap. This is how long gaps are penalised. If you don't like long gaps, just increase the extension gap penalty. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring.
Default values:
- BLASTP: 1
- BLASTX: 1
- BLASTN: 1
SCORES:
Setting this option to any number available in the menu allows you to set to maximum number of reported scores in the output file.
The default is 25.
ALIGNMENTS:
Setting this options to any number available in the menu allows you to set the maximum number of reported alignments in the output file.
The default is 15.
GAPALIGN:
This is a true/false answer that tells the program the perform optimised alignments within regions involving gaps. If set to true, the program will perform an alignment using gaps. Otherwise, if it is set to false, it will report only individual HSP where two sequence match each other, and thus will not produce alignments with gaps.
(N.B. HSP means High-Scoring Segment Pair. Local alignments with no gaps that achieve one of the top alignment scores in a given search).
The default is true.
