User: Micans

gravatar for Micans
Micans270
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6 years, 7 months ago
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Posts by Micans

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Web-Based Visualization Tools For Protein Interaction Networks
... You could try BioLayout. ...
written 7.5 years ago by Micans270
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Comment: C: Data Too Big To Be Stored In Memory: Common Options
... Your question is underpowered. A more specific description will enable more specific answers. ...
written 7.5 years ago by Micans270
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Answer: A: Data Too Big To Be Stored In Memory: Common Options
... There are good answers already; if you can, always stream or chunk the data, avoid databases. You've given us very little information about the actual problem at hand though. Quite often the particular problem leads to particular solutions. In network analysis one could work with pruned networks, wh ...
written 7.5 years ago by Micans270
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Answer: A: Five Step Method For Small Rna Analysis.
... A lot of software already exists that does this. This does not imply it is not a good project. Rather, it could help you in increasing your understanding of the requirements. In our lab we've written software for all five steps. I'll just highlight two programs that do the first three steps in you l ...
written 7.7 years ago by Micans270
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Answer: A: Multiple Sequence Alignment Of 3' Utr
... It's been a while since I looked at this, but we have used LAGAN to align UTRs (http://lagan.stanford.edu/lagan_web/index.shtml). It is optimized for non-coding, and other poorly conserved regions of the genome. ...
written 8.3 years ago by Micans270
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Comment: C: Ethical Issues In Bioinformatics
... If a programmer is not consciously aware of a specific patent, is this ignorance? There are millions of patents, and it is well established that programmers should not try to sift through them. Any substantial piece of codes is likely to infringe on hundreds of patents. The only ethical issue with p ...
written 8.4 years ago by Micans270
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Comment: C: How To Find Mirnas In Deep Sequencing Data When Genomic Sequence Unavailable
... I forgot, you could also use http://www.ebi.ac.uk/enright-srv/MapMi/, developed in the Enright lab. It is a tool "designed to locate miRNA precursor sequences in existing genomic sequences (e.g Ensembl and Ensembl Metazoa), using potential mature miRNA sequences as input". This would be one way to g ...
written 8.6 years ago by Micans270 • updated 8 months ago by RamRS27k
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Answer: A: How To Find Mirnas In Deep Sequencing Data When Genomic Sequence Unavailable
... Some ideas from our lab: 1) Do you have cDNAs / ESTs for your species? You could map to those, see whether they are primary transcripts with hairpin structures. 2) At 100bps you might still get hairpins in your reads. 3) Stack reads, look for clean 5' start sites in the stack. 4) See whether there a ...
written 8.6 years ago by Micans270
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Comment: C: A Query For The Program Of Tribe-Mcl
... The answer is no I guess. MCL does fairly well at the multi-domain sequence problem, but it is completely oblivious to the domain structure; it knows only about the BLAST scores. This means that MCL is able to utilise those BLAST scores relatively well (and I am sure other cluster algorithms do too) ...
written 8.6 years ago by Micans270
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Answer: A: A Query For The Program Of Tribe-Mcl
... Author of MCL here. The 'tribe' part of Tribe-MCL is the layer outside the clustering algorithm that does data preparation and mapping of labels, in the context of protein sequence similarity analysis. This functionality has for quite a while now been natively supported in the MCL software. You can ...
written 8.6 years ago by Micans270 • updated 8 months ago by RamRS27k

Latest awards to Micans

Commentator 7.5 years ago, created a comment with at least 3 up-votes. For C: Data Too Big To Be Stored In Memory: Common Options
Appreciated 7.5 years ago, created a post with more than 5 votes. For C: Data Too Big To Be Stored In Memory: Common Options
Good Answer 8.6 years ago, created an answer that was upvoted at least 5 times. For A: A Query For The Program Of Tribe-Mcl
Appreciated 8.6 years ago, created a post with more than 5 votes. For A: A Query For The Program Of Tribe-Mcl
Teacher 8.6 years ago, created an answer with at least 3 up-votes. For A: A Query For The Program Of Tribe-Mcl
Teacher 9.1 years ago, created an answer with at least 3 up-votes. For A: Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
Appreciated 9.1 years ago, created a post with more than 5 votes. For A: Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?

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