User: Sujai Kumar

gravatar for Sujai Kumar
Sujai Kumar240
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240
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Location:
United Kingdom
Website:
ylog.org
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Last seen:
7 months, 1 week ago
Joined:
9 years ago
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Posts by Sujai Kumar

<prev • 20 results • page 1 of 2 • next >
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Comment: C: How To Make A Blast Database With Taxonids From Ncbi Query.
... I'm getting the same error when using makeblastdb with the -taxid_map option ...
written 2.7 years ago by Sujai Kumar240
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Has anyone used GET_HOMOLOGUES
... Has anyone used GET_HOMOLOGUES for pan-genome protein conservation/ortholog analysis? http://www.ncbi.nlm.nih.gov/pubmed/24096415  It's supposedly better than orthoMCL? If you have used it - would you mind sharing your opinion of it and if you'd prefer it to orthoMCL (and why). Thanks! ...
conservation ortholog protein comparative genomics written 4.9 years ago by Sujai Kumar240 • updated 21 months ago by bcontreras0
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Answer: A: How To Extract Target Domains/Sequences From Interproscan Tsv Results
... Grep the lines in the TSV file with the search terms of interest (eg NBS-ARC) grep NBS-ARC interpro.tsv >NBS-ARC.tsv Extract the sequence ID, start, stop columns cut -f1,7,8 NBS-ARC.tsv >NBS-ARC.bed Use bedtools getfasta to extract the fasta sequences with those coordinates bedtools getf ...
written 5.2 years ago by Sujai Kumar240
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Comment: C: Lastz Genome Alignment Tool: How Does Softmasking Work?
... Thanks for this. I already have masking info (from RepeatMasker). From what I can tell LASTZ wants the coordinate files if you want to do soft masking. I can do hard masking on my own by replacing with Ns but what I really want is to avoid masked regions during seed finding, and allow masked regions ...
written 5.2 years ago by Sujai Kumar240
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Comment: C: Lastz Genome Alignment Tool: How Does Softmasking Work?
... Thanks for the (potential) confirmation and suggestion for contacting the author. I'll do that ...
written 5.2 years ago by Sujai Kumar240
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Lastz Genome Alignment Tool: How Does Softmasking Work?
... I need to do a whole genome alignment on a largish metazoan (~1.8 GBp), and the sensible approach seems to be to mask the repetitive alements before doing that so that the number of all versus all seed matches is reduced. The Lastz whole genome alignment tool has a softmasking option where masked r ...
alignment written 5.2 years ago by Sujai Kumar240 • updated 14 months ago by Martin Stervander10
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Answer: A: How To Get The Result Which Mismatch 1 To The Query Sequence By Nucleotide-Nucl
... I think whenever I've seen that error, the query fasta file has had problems: can you check for blank sequences (i.e. no sequence after a line beginning with ">"); or tabs in the fasta header non-standard line endings (Win/DOS endings on Linux/OSX etc) On a side note - I seem to remember seei ...
written 6.1 years ago by Sujai Kumar240
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Answer: A: Error When Using Makeblastdb On A Large File
... I agree that the OP should specify the full command and error (thanks Istvan) - but just in case this helps: makeblastdb gives an error if there are any tabs or other weird characters in the fasta file. Check your sequence headers, and replace all weird spaces with ordinary spaces. I use the foll ...
written 6.5 years ago by Sujai Kumar240
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Answer: A: Augustus Training Time
... Try the autoAug.pl script that comes with Augustus 2.5.5 in scripts: autoAug.pl --singleCPU --useexisting --genome=genome.fasta --species=speciesname --cdna=EST.fasta --trainingset=genome.gff3 We get the genome.gff3 training set from the output of a first-pass run of MAKER using: 1. EST data (if ...
written 6.8 years ago by Sujai Kumar240
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Answer: A: Parallelization Efficiency And Memory Usage Of Abyss, Allpaths-Lg
... Hi David One data point for your answer: Genome size: ~100Mbp metazoan Insert size: ~300 bp Tech : 100bp Illumina paired end HiSeq2000 V3 Num Reads : ~140 M pairs` ABySS 1.3.3 Took 6 hours on a 32 core machine. The read set was split into 20 interleaved files (if you split into interleaved fa ...
written 7.0 years ago by Sujai Kumar240

Latest awards to Sujai Kumar

Popular Question 18 months ago, created a question with more than 1,000 views. For Bincons - Does Anyone Know Where One Can Get A Copy?
Popular Question 18 months ago, created a question with more than 1,000 views. For Has anyone used GET_HOMOLOGUES
Supporter 19 months ago, voted at least 25 times.
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Local Blast: Querying A Single Sequence Without Input File. Possible ?
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Lastz Genome Alignment Tool: How Does Softmasking Work?
Appreciated 5.1 years ago, created a post with more than 5 votes. For A: Make A Custom Blast Library Using The Output Of Another Blast Result
Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: Make A Custom Blast Library Using The Output Of Another Blast Result
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Local Blast: Querying A Single Sequence Without Input File. Possible ?
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Make A Custom Blast Library Using The Output Of Another Blast Result

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