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  • FASTA Viewer

    Hi all,
    I have several large FASTA files and i wanted to know if there is a FASTA visualizer for Windows or Linux?

    Thanks in advance.

    Regards,
    Ashwin

  • #2
    Ashwin,

    FASTA files are simply plain text files; they could be opened with any text editor. What do you wish to do with these files? There isn't really much to "look" at in a FASTA file, it's just a long string of DNA sequence (or RNA or protein).

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    • #3
      Hi,
      I wanted to search for a sequence in a FASTA file, for e.g the sequence could be

      GGTTCCGCTTTCCACTGCTGCCGCCAGTCGGCCTGAGATGCACTGGCCTCGGCCTCAGAGGAGGCAGTCGCTGACACCTGGCTCCAGGTCCTGGAATCCGGAGGGGCCTCTGGGCCACCGG

      OR

      GGTTCCGCTTTCCACTGCTGCCGCCAGTCGGCCTGAGATGCACTGGCCTCGGCCTCAGAGTAGGCAGTCGCTGACACCTGGCTCCAGGTCCTGGAATCCGGAGGGGCCTCTGGGCCACCGG

      If the FASTA was viewable, then i could do a find for confirmation, i.e. to confirm that the searching code is working fine.

      Does the program FASTA search for a sequence within a FASTA file.

      Ashwin

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      • #4
        If you do a simple text search with a text editor, you might miss it since the file contains linebreaks.

        I'd simply make a BLAST database out of the FASTA file and use BLAST to find the matching position.

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        • #5
          Hi there,
          I did run formatdb on my FASTA file but i am getting an error stating index file not found.

          Do you know the exact syntax for formatdb to convert a .fasta file into a BLAST able .fasta database file.

          Thanks in advance.
          Ashwin

          Comment


          • #6
            Legacy BLAST formatdb for nucleotide FASTA files:
            Code:
            formatdb -p F -i file.fasta
            To search:
            Code:
            blastall -p blastn -d file.fasta -i query.fasta
            Execute "formatdb --help" and "blastall --help" to see all options.

            Comment


            • #7
              Another, perhaps more user friendly approach for non bioinformaticians might be
              Artemis from the Sanger Institute.

              A good text editor, i.e. Notepad++ on Windows, might do the trick too, but watch out for
              line breaks.

              Comment


              • #8
                If you are familiar with command line terminal, you could try grep in the command line:

                Code:
                grep "yoursequence" yourfastafile
                Using the '-B 1' option will allow you to grab the header for this sequence too:

                Code:
                grep -B 1 "yoursequence" yourfastafile
                if you have a text file with each sequence on each line you can use fgrep:

                Code:
                fgrep -B 1 -f filewithlistofsequences yourfastafile
                These will produce an output to the screen if the sequence exists (or you could redirect to another file using '> output.txt'). Otherwise there will be no output. But the search will only be for exact matches, and will miss sequences with line breaks in between.
                Last edited by Kennels; 02-26-2012, 09:32 PM.

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