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using the gap coder software

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using the gap coder software

Postby grkanth » Wed Feb 15, 2006 8:49 pm

hi people,

i am new this forum. I am pleased to find this forum.

has anyone tried using the gap coder. this is small piece of software to score the gap in the DNA sequence alignment.

I tried several times but i am not getting the proper out put.
If i modify the the fasta file as per the instruction that is exported from the winclada, the gapcoder doesn't read.

please suggest solution to this if any one has used.

thanks in advance
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gapcoder

Postby twanto » Sat Mar 25, 2006 3:18 am

Gapcoder is a funny with formats. Here is my workflow to get it to work: I open my alignment in ClusalX (free alignment software) and export it from there into a PIR format. The GapCoder software has no problems with .pir files but I have never gotten it to work properly with fasta. pir would be option 2 in when you import the file into gapcoder. Hope this helps.

Nathan
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Re: using the gap coder software

Postby dlzhqx » Thu Jul 13, 2006 12:56 am

Hi, I am also new to this forum. Recently, my supervisor suggested me to use gapcoder. I try to download this programme, but I failed.
I wonder if anyone could help me for sending this programme by email? Thanks in advance. My email address: zhouqx@hotmail.com



grkanth wrote:hi people,

i am new this forum. I am pleased to find this forum.

has anyone tried using the gap coder. this is small piece of software to score the gap in the DNA sequence alignment.

I tried several times but i am not getting the proper out put.
If i modify the the fasta file as per the instruction that is exported from the winclada, the gapcoder doesn't read.

please suggest solution to this if any one has used.

thanks in advance
dlzhqx
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Postby mith » Thu Jul 13, 2006 1:22 am

he seems to have disappeared, have you tried this

http://maen.huh.harvard.edu:8080/services/gap_recoder
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Postby dlzhqx » Fri Jul 14, 2006 3:13 pm

I have tried, but...... Anyway, Thank you very much!


mithrilhack wrote:he seems to have disappeared, have you tried this

http://maen.huh.harvard.edu:8080/services/gap_recoder
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Postby el diablo » Tue Mar 06, 2007 5:29 pm

whats a gapcoder software?
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