how find the putative gen from cdna library?

Question

[alirezaei3333]

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 ?

[GenoMax]

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

[pltbiotech_tkarthi]

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

Answer 1

[lieven.sterck]

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.