Questions tagged [sequence-analysis]

Umbrella term for understanding any given nucleic acid sequence code, either as a locus, loci or genome with itself or as a comparison to comparable nucleic acid sequence code either intraspecifically or interspecifically

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Mutations in sequences relative to reference (histogram)

I have a reference sequence of amino acids that I compare other sequences to using Bio.pairwise2.align.globalmx of Biopython package (one to many compare - one by ...
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2answers
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Why PHMM is used For Protein Analysis

I am interested on how profile hidden markov model is used for protein analysis in bioinformatics. Can you guys explain why phmm is more preferable method comparing to simple MSA(Multiple Sequence ...
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Way to get genomic sequences at given coordinates without downloading fasta files of whole chromosomes/genomes first?

So I have a list of start and stop positions along chromosomes in different species, and I'd like to get the corresponding DNA sequence for each set of coordinates. In the past, I've just download the ...
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1answer
306 views

Recommendations for missing value imputation - DNA methylation data

I'm looking for some options for imputation for a high-dimensional dataset of DNA methylation (bisulfite sequencing) data. Dimensions on the order of 50-100 samples x ~500,000 CpG loci/features. I'...
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2answers
537 views

Is it wise to use RepeatMasker on prokaryotes?

I'm looking for a way to identify low complexity regions and other repeats in the genome of Escherichia coli. I found that RepeatMasker may be used for example when drafting genomes of prokaryotes (E. ...
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1answer
507 views

How to confirm exon shuffling in a gene?

Note: this question has also been asked on reddit I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, ...
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1answer
165 views

Does Prokka or gff3 change the sequence / subject ID of fasta files?

I used prokka to create a database for some fasta files but I noticed a strange difference between the prokka and fasta files. Normally the seqid for the gff3 output for prokka has seqid's that match ...
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3answers
1k views

How does blastn sort output?

I used blastn to search one a genome database for the sequences in a file. ...
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3answers
256 views

Generic HMM solvers in bioinformatics?

Hidden Markov models (HMMs) are used extensively in bioinformatics, and have been adapted for gene prediction, protein family classification, and a variety of other problems. Indeed, the treatise by ...

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