FASTA AND BLAST

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huda nawaf
huda nawaf on 14 Nov 2011
hi, are there fasta and blast functions in matlab?
thanks

Answers (3)

Walter Roberson
Walter Roberson on 14 Nov 2011
  3 Comments
Walter Roberson
Walter Roberson on 15 Nov 2011
Well, that is odd, considering that the blast* functions in that toolbox specifically include the reference,
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410.

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Lucio Cetto
Lucio Cetto on 19 Nov 2011
None of these alignment algorithms are included in Matlab.
Do not mix the "fasta" alignment algorithm with the "fasta" file format. Matlab provides fastaread and fastawrite for I/O FASTA formatted files.
In the case of the "blast" algorithm Matlab does provides a wrapper that allows you to pass the information to a locally installed blast (blastlocal), and provides a read function (blastlocalread) that will let you put the results of the alignments back in Matlab, but you will need to install the blast algorithm (provided by NCBI) by yourself. Also Matlab provides a function that allows you to submit queries to the NCBI's blast server, balstncbi (i.e. aligning against their databases). The function blastread will read the web data back into Matlab.
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huda nawaf
huda nawaf on 29 Nov 2011
thanks Lucio
I did not see this last comment , walter draw my attention to this comment.
i will see that link and that function

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Jonathan
Jonathan on 14 Nov 2011
The following commands and output says there are not such functions.
>> help fasta
fasta not found.
Use the Help browser Search tab to search the documentation, or
type "help help" for help command options, such as help for methods.
>> help blast
blast not found.
Use the Help browser Search tab to search the documentation, or
type "help help" for help command options, such as help for methods.
If you can tell us the purpose of the functions, perhaps we can answer if there are equivalent functions in Matlab.
  4 Comments
Diego
Diego on 28 Dec 2011
Did you already look at the swalign.m file located inside the bioinfo/bioinfo folder?.

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