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Forum: Bioinformatics 12-04-2018, 05:01 AM
Replies: 6
Views: 9,273
Posted By fungs
Native support

Just to complete this: NCBI Blast+ now supports SAM directly.
Forum: RNA Sequencing 12-04-2018, 03:00 AM
Replies: 2
Views: 3,336
Posted By fungs
Thx

Never thanked you for your answer. Thx!
Forum: RNA Sequencing 01-18-2011, 12:36 AM
Replies: 2
Views: 3,336
Posted By fungs
Primer design reference positions

Hello,
this might seem like a very basic question but I could not find a clear answer, yet. So I am hoping that anyone here is familiar with this matter.

I'm dealing with 16S primers for...
Forum: Bioinformatics 09-06-2010, 06:59 AM
Replies: 5
Views: 5,806
Posted By fungs
Just to let you know: Here is some evidence on...

Just to let you know: Here is some evidence on the issue. I checked different versions and engines of NCBI BLAST. This seems to be an optimization in the code that is on purpose. The effect is that...
Forum: Bioinformatics 08-27-2010, 02:21 AM
Replies: 5
Views: 5,806
Posted By fungs
Yes thanks, I counterchecked with the latest...

Yes thanks, I counterchecked with the latest BLAST+ version and found the same issue. The raw score is important to me because when I compare different aligners using the same scoring scheme should...
Forum: Bioinformatics 08-26-2010, 04:08 AM
Replies: 5
Views: 5,806
Posted By fungs
Yes, I am using BLAST+. I am currently running...

Yes, I am using BLAST+. I am currently running the latest version to see whether it makes any difference. Anyhow, this shoudn't be if it is really a bug. I couldn't find anything about it in the...
Forum: Bioinformatics 08-23-2010, 07:51 AM
Replies: 5
Views: 5,806
Posted By fungs
Blast raw score calculation

Hello,

I know this sounds strange but I am having problems to validate the BLAST raw alignment scores (not the bit scores). Here an example alignment:
...
Forum: Bioinformatics 04-09-2010, 08:03 AM
Replies: 0
Views: 1,386
Posted By fungs
Blast query masking behavior

Hi, this is about a simple alignment issue with NCBI Blast:

Does anybody know a way to make a query sequence containing masked nucleotides (N symbol) match against the reference region containing...
Forum: Bioinformatics 01-26-2010, 02:51 AM
Replies: 6
Views: 9,273
Posted By fungs
more verbose

I was aware that the script is not mature but for understanding its functionality I need some more information on its usage, e. g. what the BLAST output format should be for the program input. I was...
Forum: Bioinformatics 01-25-2010, 03:51 AM
Replies: 6
Views: 9,273
Posted By fungs
SAM(tools) and BLAST

Hi there,

I am currently trying to use different aligners for metagenomic short/medium sequences and SAM seems to be a good intermediate format for my analyses. For sensitivity reasons my current...
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