searching tools - alignment of sequences using tools (May/30/2003 )
I know that there r few search tools like BLAST and FASTA for sequence alignment,but could u please let me know how can I get the detailed information about this search tools and how these tools are useful.Where can I look for the algorithm for these tools and full interpretation of the BLAST and FASTA results?Please let me know what is this SW -search and how is it superior to rest of the two.
A countless thanks in advance.
go to NCBI website http://www.ncbi.nlm.nih.gov/BLAST/. you will find tons of information. You can also get the software from its ftp site and run it on your own computer. There are detailed information about blast output so you can write your own program to parse the results. for algorithms, you can find the original papers which describe those programs.
Hope it helps.
another literature source is the volume 266 of Methods in Enzymology from 1996.
Very detailed, lots of references. Another good book is 'bioinformatics' by
Baxevanis and Ouellette.
Another point: your speaking of 'sequence alignment', neither FASTA nor BLAST
are programmed for pure alignment purposes, just for database searches.
If you really want to say something about the possible function of a sequence,
you should run your query sequence and your FASTA/BLAST-hits through ClustalW
I hope I could help a little bit. Good luck.
With best regards,