Question

how find the putative gen from cdna library?

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5.7 years ago

alirezaei3333 • 0

i have transcriptome one of kind scorpion and i translated them to 6 frame orf. i have to find putative gens. which tools and date base will help me ?

RNA-Seq • 981 views

ADD COMMENT • link updated 5.7 years ago by pltbiotech_tkarthi ▴ 180 • written 5.7 years ago by alirezaei3333 • 0

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GAWN - Genome Annotation Without Nightmares
Annotation pipelines in 2018
http://www.yandell-lab.org/software/maker.html

ADD REPLY • link 5.7 years ago by GenoMax 147k

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Try ENSEMBL DNA or Protein BLAST servers and NCBI BLAST servers. Try also this : http://www.softberry.com/berry.phtml?topic=fgenes_plus&group=programs&subgroup=gfs

ADD REPLY • link 5.7 years ago by pltbiotech_tkarthi ▴ 180

score 0 · Answer 1 · 2019-03-21

Given that you are looking in (assembled) transcripts sequences (so not genome, right?), I suggest to go for something straightforward. What you after is often referred to as longest ORF.

Suggested tools: TransDecoder, FrameD, longest_orf.pl, ... and there are likely many others around (as well as custom scripts/implementations) . All those will take nucleotide sequences as input so no need to translate into 6 frames.