What Is A Good Visual Tool For Alignment And Viewing Of Sanger Traces?

Question

[Bigmac]

I would like to get some suggestions for relatively simple visual tools for aligning and examining Sanger sequencing data. All I am trying to do is align a bunch of traces to the mRNA/cDNA sequence for the gene. Any assistance would be much appreciated.

I currently primarily use Consed. However, it is a UNIX tool and that confuses other people. The alignment is not especially helpful either because it does not give you codons or position within a gene.

Mutation Surveyor is fairly simple to use. It aligns the traces and then tells you exactly where each position falls within the gene. It also does mutation calling, which is not very good and not even necessary for me. It's also fairly expensive."

Answer 1

[Ido Tamir]

I worked with staden screenshots in linux, but its said to work under windows also. Some things were not extremely intuitive, but it worked and it might have improved a lot since when I used it. It can also plug in different assembly algorithms if you need that.

Answer 2

[Casey Bergman]

Ido's suggestion to use Staden is the right choice for an open-source solution, but if you have funds to allocate to this task, try the SeqMan or Sequencher.