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Old 02-13-2012, 12:50 PM   #1
gwilymh
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Default 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?
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Old 02-13-2012, 12:58 PM   #2
jts
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Try the program fastaFromBed in bedtools:

http://code.google.com/p/bedtools/
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Old 03-03-2015, 08:07 PM   #3
jalapea
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Default 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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Old 03-04-2015, 02:54 AM   #4
GenoMax
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Quote:
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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