SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 8 of 8
Search took 0.00 seconds.
Search: Posts Made By: *#1*
Forum: Bioinformatics 04-03-2012, 10:20 AM
Replies: 2
Views: 2,933
Posted By *#1*
How to circularize plasmid assembly

Hi,
My assembly resulted in a single contig, which is linear. How do I check where is the complimentary sequences on the ends so that I could circularize the plasmid? Is there a tool that can do...
Forum: Bioinformatics 03-29-2012, 03:37 PM
Replies: 2
Views: 3,202
Posted By *#1*
Thank you for the reply. I can certainly do...

Thank you for the reply. I can certainly do simple Perl and Python, but I am not sure how to approach the problem. If you have ready to use scripts, I'd appreciate your posting them here.
Thanks!
Forum: Bioinformatics 03-28-2012, 07:21 PM
Replies: 3
Views: 2,110
Posted By *#1*
In some aligners there is a permissivity option...

In some aligners there is a permissivity option that defines to how many locations a read can be mapped to. By default it is usually 1, i.e. once a good match is found, teh read gets mapped to it and...
Forum: Bioinformatics 03-28-2012, 07:15 PM
Replies: 3
Views: 2,509
Posted By *#1*
I also suggest Muscle...

I also suggest Muscle http://www.drive5.com/muscle/
Forum: Bioinformatics 03-28-2012, 07:11 PM
Replies: 1
Views: 1,463
Posted By *#1*
Normally NGS aligners would produce some sort of...

Normally NGS aligners would produce some sort of .gff or .bed file that would contain information about indels, so you would simply need to grep for "del" or "ins" or whichever is the tag. So, you...
Forum: Bioinformatics 03-28-2012, 04:56 PM
Replies: 2
Views: 3,202
Posted By *#1*
How to trim multiple alignment?

I have a specific problem. We want to discover isoforms of a gene based on long reads. We have a population of overlapping sequences all under 1000bp. I aligned them with Clustal, and now would like...
Forum: Bioinformatics 10-05-2011, 01:09 PM
Replies: 1
Views: 1,904
Posted By *#1*
NGS read mapper that would extend the seeding contig.

The biological problem I am solving is to try finding an integration site for a certain sequence into a large mammalian genome. I know the sequence of the integrating element, and it is not that big...
Forum: Bioinformatics 10-19-2010, 05:35 PM
Replies: 4
Views: 3,699
Posted By *#1*
Exclamation Non-commercial SNP calling soft

I noticed that information on SNP calling and SNP discovery (especially!) software for NGS is quite scarce:confused:. Are there any good tools available from non-commercial sources? Could you suggest...
Showing results 1 to 8 of 8

 


All times are GMT -8. The time now is 01:04 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO