User: Monzoor

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Monzoor300
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8 years, 11 months ago
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Posts by Monzoor

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Distinguishing Between Real Dna Strings Vs Random Dna Strings
... Guess it was fun to do. But did you try your method on structured english text vs randomly generated alphanumeric strings ? Me too just curious. ...
written 8.9 years ago by Monzoor300
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Comment: C: Segregating Metagenomic Sequences In Prokaryotic And Eukaryotic Groups.
... I have tried c-Bar and found its performance to be good with sequences that are atleast of 2000 bp lenght. The accuracy with NGS reads (length 100-400) is around 50% which in my opinion can be obtained using toss of a coin. Being an author of SPHINX, I can only ask you to try the same. FYI, SPHINX h ...
written 10.1 years ago by Monzoor300
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Comment: C: Question About The Choice Of Reference Genomes For Mapping Metagenomics Reads
... I agree. Will be careful next time. ...
written 10.2 years ago by Monzoor300
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Comment: C: Algorithms Accuracy Vs Compute Requirements
... I agree. Nevertheless, I still find that scientists now are not interested in developing algorithms (especially with respect to NGS data) that can smartly sift through thousands of solutions and get the end-user a near optimal solution using minimal compute power. ...
written 10.2 years ago by Monzoor300
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Comment: C: Algorithms Accuracy Vs Compute Requirements
... Sure Eric. Got your message. Will be careful next time. Any ways do you know of any nice fora where I can ask/discuss and get perspectives on such topics. Thanks in advance ...
written 10.2 years ago by Monzoor300
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Algorithms Accuracy Vs Compute Requirements
... A lot of algorithms developed for NGS data (especially metagenomic) analysis need huge compute power. Moreoever there seems to be a race for developing algorithms for clusters, parallel versions etc. Though I agree that compute power is not that astronomically expensive now, is it not true that the ...
algorithm hardware written 10.2 years ago by Monzoor300 • updated 9.8 years ago by lh332k
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Question About The Choice Of Reference Genomes For Mapping Metagenomics Reads
... My first question is what are the uses/applications of reference genome mapping? Second, assuming that I have sequenced an environmental sample for metagenomic analysis, since I have no idea of its taxonomic composition, how would I decide which genome I should use as a reference for mapping my rea ...
genome metagenomics mapping written 10.2 years ago by Monzoor300 • updated 7.1 years ago by Biostar ♦♦ 20
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Comment: C: Segregating Metagenomic Sequences In Prokaryotic And Eukaryotic Groups.
... Hey this is akin to saying "BLAST and MEGAN are the last and the only resort". I was expecting this question to spawn a few novel ideas that help researchers in resource poor settings. In other words, metagenomics analysis seems currently restricted to groups that can afford huge compute resources. ...
written 10.2 years ago by Monzoor300
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Comment: C: Segregating Metagenomic Sequences In Prokaryotic And Eukaryotic Groups.
... MG-RAST bases its phylogenetic inferences by blasting sequences against 16S/18S/28S etc reference sequences and finding relative abundance of various taxa. What it does not give is a read by read analysis of taxonomic inferences. Anyways, new insect sequences are absent from their database in any fo ...
written 10.2 years ago by Monzoor300
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Comment: C: Segregating Metagenomic Sequences In Prokaryotic And Eukaryotic Groups.
... Assuming I find 10-15% contamination with a random sampling, I still need a solution for quantifying/separating these sequences from the entire data set. Planning to use MGRAST for functional annotation instead of using a gene prediction method. Maybe I need to use something like Metagene for gene p ...
written 10.2 years ago by Monzoor300

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