Moderator: iw9oel_ad

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Posts by iw9oel_ad

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Answer: A: Is Bam One-Based Or Zero-Based?
... As you point out, the SAM spec is unambiguous on this; BAM data are 0-based and SAM data are 1-based (sections 1.2 and 3.2). A feature at base 0 in a BAM file will be at base 1 when the data are exported as SAM. ...
written 5.3 years ago by iw9oel_ad6.0k
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Answer: A: Please Recommend A *Good* Ontology Editor For Biomedical Ontologies
... I use Protege for OWL ontologies because I find OBOedit's UI, shall we say, idiosyncratic. Protege has nice features like reasoner plugins that can spot errors and make inferences. However, it is complex and takes some time to learn. The documentation is quite good, which helps. I'm certainly not a ...
written 5.4 years ago by iw9oel_ad6.0k
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Comment: C: In Writing Biomedical Applications, Which Disadvantages Of R/Advantages Of Pytho
... "Full object orientation" isn't a meaningful term. In fact R has more object systems than many languages; 3 at the last count, these being S3, S4 and R5. The S4 model, having a generic functions and multiple dispatch, is arguably superior to Java's single-dispatch model for writing flexible code. ...
written 5.7 years ago by iw9oel_ad6.0k
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Comment: C: Scoring Matrix Is It Always A Symmetrical One ?
... I didn't think about phylogenetic cases. Thanks for catching that. ...
written 5.9 years ago by iw9oel_ad6.0k
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Answer: A: Scoring Matrix Is It Always A Symmetrical One ?
... In general there is no reason why a scoring matrix used in dynamic programming has to be symmetric. However, the most commonly used ones are symmetric, for example when making an alignment. Usually a scoring matrix is chosen because it models a biological situation. If your biological model requires ...
written 5.9 years ago by iw9oel_ad6.0k
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Comment: C: Scoring Matrix Is It Always A Symmetrical One ?
... Presumably you mean a scoring matrix in the context of sequence alignment? Please try to improve your questions. ...
written 5.9 years ago by iw9oel_ad6.0k
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Comment: C: Simulate 1, 3 Copies
... If you have more information to add, please edit your original question instead of putting it here. This helps maintain the quality of Biotstar's answers. Thanks. ...
written 5.9 years ago by iw9oel_ad6.0k
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Answer: A: How Can I Determine The Coding Sequence Of A Gene, Given The Genbank Accession N
... Locus NM_001129809 in Genbank is Strongylocentrotus purpuratus lefty (LOC577374), mRNA. 'mRNA' is an abbreviation for 'messenger RNA'. The Genbank entry is annotated with a CDS feature at bases 112..1311. 'CDS' is an abbreviation for 'coding sequence'. Is the problem that you do not understand the c ...
written 5.9 years ago by iw9oel_ad6.0k
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Comment: C: Entering Into Bioinformatics Domain
... What books and topics did you find while doing the literature search for your project? In what way were they not useful? ...
written 5.9 years ago by iw9oel_ad6.0k
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Comment: C: Cut The Reads Of A Paired End Fastq File
... See Rule 4 in the document linked from the very top of the page. Or put the terms 'trim fastq' into any search engine. Answer is on the first page. ...
written 5.9 years ago by iw9oel_ad6.0k

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