User: mcsimenc

gravatar for mcsimenc
mcsimenc10
Reputation:
10
Status:
New User
Location:
California, USA
Last seen:
8 months, 2 weeks ago
Joined:
2 years, 10 months ago
Email:
m*******@gmail.com

Posts by mcsimenc

<prev • 5 results • page 1 of 1 • next >
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NCBI's tbl2asn for sequin files for GenBank submissions - what else does the program do in the system?
... Hello, I am making a MacOS GUI wrapper app for some of tbl2asn's functionality. The app is containerized a.k.a. sandboxed, which means it only has permission by default to read and write within the bounds of the app's space. tbl2asn runs successfully, as expected, from within the app when sandboxin ...
sandboxing tbl2asn genbank macos written 8 months ago by mcsimenc10
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Comment: A: Assembling PacBio reads using a reference genome
... Bump! Anyone know of any methods for the original question not listed here that may have shown up in the past 17 months? We are needing to assemble genomes from plant cultivars that are different from the cultivar for which 2nd/3rd round genome assemblies are publicly available. We are hoping to fi ...
written 10 months ago by mcsimenc10
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Where can I find GMAP? All links appear dead. Was the project abandoned?
... I want to use GMAP for my project, because Exonerate doesn't seem to be able to do multiprocessing/threading. I see the repo: https://github.com/juliangehring/GMAP-GSNAP has not been active and at the top states: *UNMAINTAINED and OUTDATED*: This was an inofficial archive of GMAP-GSNAP releases. Pl ...
gmap alignment gsnap software availability written 13 months ago by mcsimenc10 • updated 13 months ago by genomax74k
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Interpreting jmodeltest2 using transposon sequences results
... Dear Biostars community, I want to estimate divergence between two long terminal repeats from a single LTR retrotransposon, which are assumed to be identical when a new element is inserted. I have estimated substitutions per site this using baseml, selecting a model of sequence evolution more or le ...
model transposon jmodeltest2 long terminal repeats written 2.5 years ago by mcsimenc10
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PASTEC repeat classification software (part of REPET) help needed
... I am trying to use [PASTEC][1] with my genomes on a cluster running TORQUE. The program's version of parallelization is splitting the input sequences in to batches and submitting many individual jobs to the cluster. I have not figured out how to (1) limit the number of jobs submitted or (2) increas ...
repet parallel repeat classification pastec torque written 2.9 years ago by mcsimenc10

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