The study of genomes, the entire hereditary information of an organism.

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Sequence alignment scoring

The following table is from Deonier's text Computational Gene Analysis at p. 152. This is an exercise in global sequence alignment and scoring of alternative sequences. The text proposed a solution ...
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Comparative cost of RNA-seq vs sequencing full length cDNAs

I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data ...
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Predicting host-pathogen gene interaction networks

Background What we have are: ~20 genome sequences for a host species that come with gene annotations Several sequenced genomes for parasite/pathogens of these hosts Question What are the ...
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Too few transcripts from transcriptome assembler Oases

I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks. Here is my running command: ...
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Referencing the homologous chromosomes

There exist a co-ordinate system from chromosomes like "12p11.3". In this system, first integer range from 1 to 23 i.e it takes homologous chromosomes as a pair. If we want to distinguish among ...
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Paired-end mapping exercise

Pair-end mapping (PEM) is a technique that allows to detect structural variants in DNA by obtaining paired-end reads and the comparison of their positions in a reference genome. Then among libraries ...
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“Gold standard” for CNV detection methods?

Is there a generally accepted "gold standard" for testing the performance of CNV detection methods? I'm interested both in learning about existing datasets that may serve as gold standards for CNV ...