Consensus by aligning and extending the sequences
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5.5 years ago
BDK_compbio ▴ 130

I am trying to align and extend some sequences to get a larger consensus sequence. Here is a toy example of my problem

 ACTTACTGTAGTAGA
GTA-AGATGCGATGAGGAGAT-GAGAAATG
GATG--ATGAGGAGATAGAGAAATGATTATA
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ACTTACTGTAGTAGAGATGCGATGAGGAGATAGAGAAATGATTATA


I tried with different MSA tools, but most of them are trying to align the sequences from the first position. I am wondering if I am not aware of any tool that will solve my problem.

fasta msa alignment • 958 views
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5.5 years ago
h.mon 34k

Try CAP3, or GAP4 / GAP5.

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Thanks !! I will try them