How to align the sanger sequenced fragments against human reference gene?

Question

[bioinforesearchquestions]

Hi folks,

I have been provided sequence file from Sanger sequencing platform. It has 12 exons, so the technician has captured 5'UTR+exon1, exon2, exon3,.......exon12+3'UTR. He asked me to align with the human reference gene and try to find the variants from it. He provided me many fragments of sequence belonging to these 12 exons for he did forward and reverse sequencing for each of the 12 regions in multiple fragments.

I am planning to do following steps, -> Create bowtie2 index for the human reference gene -> I have fasta sequence of each fragments (for 12 exons+5'UTR and 3'UTR). -> do alignment with the reference gene against the fasta sequence? -> extract the consensus region and identify the variants within the exons. Or -> just use BLAST. Any suggestions are welcomed to achieve this task?

[GenoMax]

Nothing this complex should be needed. Why not try a simple multiple sequence alignment program? Start with JalView/clustalX/MEGA.

Answer 1

[WouterDeCoster]

Note that specific tools exist for sanger sequencing. I can recommend novoSNP, a tool developed in our department, which performs alignment and automatic variant scoring.