My team worked on GS-FLX to construct cDNA Library of an organism as the first time. We have contigs now. Since we blast our contigs, usually we see that the sequences are pretty close to similar organisms. But there are some broken parts of individual genes also. And I am interested in some of these genes.
When I try to align, assemble on BioEdit, I see that there are so many different bases on the same gene parts (which were checked on NCBI-Blastx). On the other hand, I want to fill the gaps. I read lots on the forums, tried to install softwares (so less available for Windows), but I could not get any good data. I have some questions?
1- Is it possible to see different bases in the same gene parts? which one would be reliable, how to decide?
2- This is de novo work, so I don't have exact gene infos. How could I see that the full lengths are right or wrong?
3-Is there any tips about the useful softwares?
4- Normally the sequence analysis show the peaks, and it is easy to pick the right bases. Is there anyway to see the right bases?