Contigs problem - (Jul/05/2013 )

Hi,
can you please answer my Q?
Here's prob.
I am trying to make contigs using CLC work Bench.
I have three sequences after curating( removing Vector Sequence). I tried to match them with Reference sequence available at NCBI. Individual sequences are showing conflict region but final sequence is with consensus to reference sequence and automatically correcting conflict regions. So my three sequences when assembled in CLC work Bench shows same sequence as reference(conflict regions are automatically getting adjusted to referece.).


I am using trial version of CLC workBench. I tried CAP3 and Dragon but could not get/understand relevant information out of it. If anybody knows better software/Knowhow please mention!!!!!!!!

Thank You.

I've been using DNA Baser (trial) for doing contigs without reference sequence, and it was the only software that didn't cut/insert gaps in my sequences to make the contig. It allows to do contigs even using the ab1 files, so in case you have overlapping of sequences is very helpfull.

Thanks.
I have tried to remove vector sequence by CLC software but it did not do it properly so I manually removed vector sequence by matching with BLAST search. Now I have three FASTA files which I want to use for contigs making. Can I use DNA Baser for it. I saw DNA baser I gives pretty good graphic look, but requires SCF file format.

I never did with FASTA but I just tried and it worked. Otherwise, you can check Unipro UGENE (free), I'm pretty sure I saw something like you want while watching the tutorials in youtube
http://www.youtube.com/user/UniproUGENE/videos