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how find the putative gen from cdna library?

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
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updated by pltbiotech_tkarthi pltbiotech_tkarthi • written by alirezaei3333 • alirezaei3333

1 answer

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.

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written by lieven.sterck lieven.sterck

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