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Forum: Bioinformatics 07-19-2011, 07:25 AM
Replies: 0
Views: 1,182
Posted By nitinkumar
Phylogeny

I want to make phylogeny of contigs of 10 strains of sinorhizobium produced from Newbler software using a already mapped genome of sinorhizobium medicae. I have no idea how to do this. please give...
Forum: Bioinformatics 05-21-2011, 06:38 PM
Replies: 0
Views: 2,566
Posted By nitinkumar
Consensus sequence

I compare some 454 reads with a reference genome using blastn with ungapped alignment. I have converted the blast reslts into fasta format. Now I want to convert the reads (output of blast) into...
Forum: Bioinformatics 05-16-2011, 08:17 AM
Replies: 8
Views: 2,133
Posted By nitinkumar
The contigs are of the rhizobium strains and...

The contigs are of the rhizobium strains and blast report shows the position where i m getting this type of results have the neighboring nucleotides exactly the same as with query. So I m pretty sure...
Forum: Bioinformatics 05-16-2011, 04:28 AM
Replies: 8
Views: 2,133
Posted By nitinkumar
Thanks for the reply and I am getting these...

Thanks for the reply and I am getting these results because of 454 sequencing errors, the query sequence is the gene of rhizobium bacteria and the subject is the sequence from matching contigs. I...
Forum: Bioinformatics 05-12-2011, 09:15 AM
Replies: 8
Views: 2,133
Posted By nitinkumar
Yes I have tried bioperl. but I am not able to do...

Yes I have tried bioperl. but I am not able to do that. I can extract the fasta sequences from these files only..
Forum: Bioinformatics 05-11-2011, 05:17 PM
Replies: 8
Views: 2,133
Posted By nitinkumar
blast results

I want to edit a blast file in such way that if the query sequence has a gap, that should also comes in the reference sequence like if blast output shows:

query: aa-gcaa
...
Forum: 454 Pyrosequencing 03-25-2011, 07:04 AM
Replies: 3
Views: 1,923
Posted By nitinkumar
Post 454 Mapper

I want to do the sequencing based on reference genome using gsMapper. I know the commands, but I don't know how to analyse the results. Can any body help me in this???
Forum: Bioinformatics 02-23-2011, 02:24 PM
Replies: 4
Views: 2,178
Posted By nitinkumar
Data consist of shotgun reads and 8 Kb paired...

Data consist of shotgun reads and 8 Kb paired ends. the coverage of some of the contigs is lower than the 20. my reference genome is 7.5 Mb and all the scaffolds show the relationship with the...
Forum: 454 Pyrosequencing 02-19-2011, 12:04 PM
Replies: 1
Views: 2,281
Posted By nitinkumar
Scaffolds

I want to compare the scaffolds with the reference sequence and analyze the order and orientation. Can any body help me in this? also can we close gaps in the scaffolds using bioinformatics approach
Forum: Bioinformatics 02-17-2011, 06:44 PM
Replies: 4
Views: 2,178
Posted By nitinkumar
Smile 454 data

what you guys thinks of a bacterial data which consist 11 scaffolds, 629 contigs with 7.5 MB (no of contigs). please tell me the criteria for choosing the correct data like what should be the size of...
Forum: Introductions 02-17-2011, 06:28 PM
Replies: 0
Views: 1,022
Posted By nitinkumar
Hello EveryOne

Hello,

I am first year Ph.D student from University of York. I am working on population genomics of a bacterial species. I am using 454 technology for sequencing the bacterial strains.

Cheers...
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