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Old 12-19-2012, 12:49 AM   #1
honey
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Default extracting seq from viral genome

I have coordinates of a viral genome and would like to extract seq from viral genome. Is there a tool or easy way to upload the txt file of ordinates and it will give me seq (equal to what do in biomart or UCSC genome page for human genes)

Thanks

honey
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Old 12-19-2012, 03:09 AM   #2
dariober
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Quote:
Originally Posted by honey View Post
I have coordinates of a viral genome and would like to extract seq from viral genome. Is there a tool or easy way to upload the txt file of ordinates and it will give me seq (equal to what do in biomart or UCSC genome page for human genes)

Thanks

honey
If you have the reference genome in FASTA format and the coordinates in BED format (chrom <tab> start <tab> end) you can you use bedtools getfasta:

Code:
bedtools getfasta

Tool:    bedtools getfasta (aka fastaFromBed)
Version: v2.17.0
Summary: Extract DNA sequences into a fasta file based on feature coordinates.

Usage:   bedtools getfasta [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> -fo <fasta> 

Options: 
	-fi	Input FASTA file
	-bed	BED/GFF/VCF file of ranges to extract from -fi
	-fo	Output file (can be FASTA or TAB-delimited)
	-name	Use the name field for the FASTA header
	-split	given BED12 fmt., extract and concatenate the sequencesfrom the BED "blocks" (e.g., exons)
	-tab	Write output in TAB delimited format.
		- Default is FASTA format.

	-s	Force strandedness. If the feature occupies the antisense,
		strand, the sequence will be reverse complemented.
		- By default, strand information is ignored.
Does it help?
Dario
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Old 12-19-2012, 09:27 AM   #3
swbarnes2
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samtools faidx will do that too, but one at a time. So embed it in some kind of shell script to get a bunch.
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Old 12-20-2012, 04:44 AM   #4
honey
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Default extracting viral seq

Thanks that was helpful !!!
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