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Forum: Bioinformatics 01-13-2011, 08:27 AM
Replies: 2
Views: 3,340
Posted By Salmon
Why is ML/NJ phylogeny different from SNP tree?

Greetings.

I am working on a bacterial genome. We have determined the complete genome sequence of this genome and want to study the evolutionary relationship of my genome and its VERY CLOSE...
Forum: Bioinformatics 09-14-2010, 09:32 PM
Replies: 5
Views: 2,712
Posted By Salmon
Dear all, Many thanks for your wonderful...

Dear all,

Many thanks for your wonderful replies. ALL are helpful! I have calculated dN/dS either and all results are reasonable, but could be slightly different between genomes.

This is my...
Forum: Bioinformatics 09-12-2010, 08:24 PM
Replies: 5
Views: 2,712
Posted By Salmon
Question help (!!!!): snynonous and nonsynonymous in bacteria

Dear all,

I have several bacterial strains (very closed to each other) and want to compare SNPs between any two genomes.
several steps in my analysis:
1. mummer (nucmer) to do alignment and...
Forum: 454 Pyrosequencing 04-09-2009, 08:36 AM
Replies: 2
Views: 2,961
Posted By Salmon
Really helpful! millions thanks ...

Really helpful! millions thanks ...
Forum: 454 Pyrosequencing 04-08-2009, 11:59 AM
Replies: 2
Views: 2,961
Posted By Salmon
454 titanium sequence company

Hello, we want to sequence whole genome on 454 titanium platform in a sequence company. Can any body recommend a company besides 454 life science to us?
Thanks a lot.
Forum: 454 Pyrosequencing 03-19-2009, 08:33 AM
Replies: 2
Views: 1,873
Posted By Salmon
Hi Rao, Thank you very much for your help. ...

Hi Rao,

Thank you very much for your help.
:)
Forum: 454 Pyrosequencing 03-18-2009, 02:36 PM
Replies: 2
Views: 1,873
Posted By Salmon
Want to generate more data to fill in gaps

Hello,
This might be a stupid question.
We are currently working on a ~5M bacterial genome assembly. Our reads data is ~8X coverage, 454 sequencing. The coverage is kind of low. So we used...
Forum: 454 Pyrosequencing 02-04-2009, 09:34 AM
Replies: 4
Views: 4,630
Posted By Salmon
454 sequencing data coverage

Dear All,

I am currently working on 454 sequencing data. The average length of reads is ~200bp, and coverage is ~8-10X.

Does anybody tell me how the data coverage is? Is it ok or not?...
Forum: 454 Pyrosequencing 01-22-2009, 09:13 AM
Replies: 3
Views: 4,951
Posted By Salmon
Homopolymer error in 454 sequencing data

Hello,
I am currently working on genome assembly. our reads data is from 454 sequencing. First we assembled contigs using Newbler. However, when we compared our built genome with a reference genome...
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