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Old 07-19-2009, 06:25 PM   #1
navin_elango
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Location: Indianapolis

Join Date: Mar 2009
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Default Overlap Graph

Dear All,

I have ~ 100000 DNA sequences in a fasta file. I am interested in finding the overlap graph of these sequences. I just want a simple overlap finder (which takes minOverlapLength and percentIdentityIntheOverlapRegion as inputs). The overlap will be at the end of the sequences (similar to assembly)

I have tried looking into many assembly programs. All the programs I looked gave the contigs as output. Some assembly programs gave information about the reads in each contig. But none of the assembly programs gave any information about the overlap graph, which was used to find the contigs. In addition, since assembly programs work with reads, they look for certain depth of coverage during overlap finding. I do not want this.

Could anyone point me towards a simple overlap-graph finder.

Thanks,
Navin.
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Old 01-06-2011, 10:31 AM   #2
niazi84@hotmail.com
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Hi Navin,

I am also looking for such software or script. Did you find any till now?
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Old 05-20-2013, 11:56 AM   #3
gtoal
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EDIT: My mistake. It looks like when you post on a subject, the board finds related threads - regardless of age. Looks like an old dead conversation, sorry to have accidentally resurrected it.


Quote:
Originally Posted by navin_elango View Post
Dear All,

I have ~ 100000 DNA sequences in a fasta file. I am interested in finding the overlap graph of these sequences. I just want a simple overlap finder (which takes minOverlapLength and percentIdentityIntheOverlapRegion as inputs). The overlap will be at the end of the sequences (similar to assembly)

I have tried looking into many assembly programs. All the programs I looked gave the contigs as output. Some assembly programs gave information about the reads in each contig. But none of the assembly programs gave any information about the overlap graph, which was used to find the contigs. In addition, since assembly programs work with reads, they look for certain depth of coverage during overlap finding. I do not want this.

Could anyone point me towards a simple overlap-graph finder.

Thanks,
Navin.
Unreleased as of yet, but I've just finished writing exactly this. Cn you be more specific about exactly what you're looking for as output, maybe with a line or two of examples?

regards,

Graham

Last edited by gtoal; 05-20-2013 at 11:59 AM.
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