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

[gwilymh]

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?

[jts]

Try the program fastaFromBed in bedtools:

http://code.google.com/p/bedtools/

[jalapea]

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

[GenoMax]

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?