Question: Genscan Gene Prediction
1
gravatar for Gvj
8.2 years ago by
Gvj440
Netherlands
Gvj440 wrote:

Dear all, I am trying to use genscan with multifasta file. I am getting this error:

scoring sequence... Error : calloc failed on CUM_SCORE array

with simple fasta file its working fine. I have found one link which also asking about the same thing. have you faced this problem of limitation with 2MB? how did you solve it?

genome annotation error • 3.6k views
ADD COMMENTlink modified 4.9 years ago by Biostar ♦♦ 20 • written 8.2 years ago by Gvj440
5
gravatar for Darked89
8.2 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

Genscan does not work well with multifasta. There is a Perl script by Brian Osborne run_genscan.pl which helps. Let me know if you can not get it from BioPerl/Google cache.

I am not sure about the Genscan limits of individual single fasta entries.

ADD COMMENTlink written 8.2 years ago by Darked894.2k
1

for i in {2..x}; do awk -v a="$i" 'BEGIN{RS=">"; tem="tmp"} NR==a{print a"n";print ">"$0 >tem; exit}' genome.fas ; genscan your.smat tmp >>genscan_sh.out; rm tmp; done

dirty version of my script to run it. note: 'x' in for loop is the number of fasta entry +1 . I

ADD REPLYlink written 8.2 years ago by Gvj440

Did you succeed to convert the Genscan output format to GFF and GTF ? I have found few on net but non of them is working. IF you have a parser for Fgenesh, please share it also

ADD REPLYlink written 8.2 years ago by Gvj440
1
gravatar for yfhuang
5.8 years ago by
yfhuang10
Taipei
yfhuang10 wrote:

I also meet this problem. It's sure that GENSCAN can't handle multifasta to predict gene. Therefore, multifasta should be split into single fasta. In addition, I try to short the length of input sequence. So far, the GENSCAN works well with parameter file of HumanIso.smat if the length of the input fasta is 5999940.

Hope this information is useful!!

ADD COMMENTlink written 5.8 years ago by yfhuang10
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