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  • Extracting sub-sequences from a larger DNA sequence using a file of coordinates

    Hi,

    I am looking to extract and annotate the sequences of a large number of genes from a series of very large (whole chromosome) consensus sequences.

    I have a file identifying the gene names and physical locations (.bed file) on their respective chromosome. There are too many genes to manually locate each one, so I need to find a way to automate this process.

    Does anyone know of a script or program that can extract DNA sub-sequences using a series of coordinates?

  • #2
    Try the program fastaFromBed in bedtools:

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    • #3
      extract the genes

      I'm trying to extract the genes of a chromosome that is in fasta file, you can help me on how to do a script, thanks

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      • #4
        Originally posted by jalapea View Post
        I'm trying to extract the genes of a chromosome that is in fasta file, you can help me on how to do a script, thanks
        In what format is the information about the genes (coordinates) you want to extract?

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