Question: how find the putative gen from cdna library?
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gravatar for alirezaei3333
4 weeks ago by
alirezaei33330 wrote:

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 • 131 views
ADD COMMENTlink modified 4 weeks ago by pltbiotech_tkarthi170 • written 4 weeks ago by alirezaei33330

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 REPLYlink written 4 weeks ago by pltbiotech_tkarthi170
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gravatar for lieven.sterck
4 weeks ago by
lieven.sterck4.5k
VIB, Ghent, Belgium
lieven.sterck4.5k wrote:

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.

ADD COMMENTlink written 4 weeks ago by lieven.sterck4.5k
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