Nearest genes to a sequence?

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7.4 years ago

jt358 ▴ 10

Hi all,

Quick query, one can obviously blat/blast short sequences (125bp) to see if they align to a protein coding region - but for those that don't align, is there a way to identify the nearest gene to the inputted sequence?

Cheers all

Jamie

gene blast SNP next-gen genome • 1.5k views

ADD COMMENT • link 7.4 years ago by jt358 ▴ 10

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If you have an alignment and a bed file of the genes then you could use bedtools closest. Link for closest doc.

ADD REPLY • link 7.4 years ago by GenoMax 141k

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Hey genomax2 - helpful as always

I can create a BED file in PLINK I assume, but perhaps a silly question, what does bedtools run short sequences against? I see you mention 'if I have an alignment' - does that mean I need an annotated indexed genome of my species?

Cheers

Jamie

ADD REPLY • link 7.4 years ago by jt358 ▴ 10

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Please use ADD REPLY to answer to earlier comments, as such this thread remains logically structured and easy to follow.

Also note that a bed file from plink isn't the same as a bed file in the rest of bioinformatics. What genomax2 means is an interval file containing chromosome, begin and end of every gene. You can probably convert a gtf/gff file for that.

ADD REPLY • link 7.4 years ago by WouterDeCoster 47k

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