Or, to paraphrase,

Hi guys.

I am amateur in perl, I need your help in solving one of my assignments.

In my program i have to call a fasta program using my perl script, after getting an output file of fasta, parse through it, and store the best matching sequence above a cut off point one at a time in a temporary file.

Now use this temporary file as the input to fasta and run the same process again.

Now compare the original output and the new output. If you have any additional sequences in the new fasta output file, append it to the original file, and repeat the process until (not sure about how to translte the rest of this -- Ed.) all the best sequence match above cut off is inputted to the fasta and you have the exhaustive homologous match

(Note sure if this helps or is just a reiteration of the original question. --Ed.) The input of 2nd phase to fasta is extracted from the output of the 1st fasta program.

So, for those who don't know (and that would include me from ten minutes ago), fasta "Compares a protein sequence to another protein sequence or to a protein database, or a DNA sequence to another DNA sequence or a DNA library." (reference).

Perhaps you can explain what your code is doing, and where you think it is breaking. Or, if you haven't written any code yet, tell use what you want to do is clearer terms. Are you trying to run the fast process yourself, or are you merely submitting your samples to a web front-end that is doing the processing?

Alex / talexb / Toronto

"Groklaw is the open-source mentality applied to legal research" ~ Linus Torvalds

In reply to Re: Fasta Using Perl by talexb
in thread Fasta Using Perl by FarTech

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