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Questions tagged [sequence-analysis]

The tag has no usage guidance, but it has a tag wiki.

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1answer
25 views

De novo motif discovery in protein sequences

I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a ...
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0answers
25 views

Sequencing Deciduous Plants

Firstly, I'm personally not in the field of Bioinformatics, so apologies if this is a dumb question. Does anyone know of any research that has been carried out on the sequencing of deciduous plant ...
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1answer
26 views

Codon usage analysis for whole genomes

I am new to bioinformatics. So if these questions seem you to a bit childish please forgive me. I have two queries. I am intending to perform a codon usage analysis followed by correspondence ...
4
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1answer
68 views

Tool to show DNA sequence and allowing upload of own graph data

Background We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a ...
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1answer
43 views

Fastqc- Per Base Sequence Quality

I am trying to figure out how to interpret the "Per Base Sequence Quality"? What does Position in reads (bp) mean? Also in order to draw this box-plot graphics, more than one quality scores are needed ...
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1answer
66 views

Python API for working with ENSEMBL genomes

Dear bioinformaticians, I could find two python APIs to mine ENSEMBL genome databases. There is a pyensembl which is more popular and then there is ...
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2answers
44 views

Effect of mutation in DNA sequence on transcription factor binding sites

How much does a single mutation/alteration of a nucleotide affect the presence of a transcription factor binding site (TFBS)? I am from computer science background(Obviously). I want to make a ...
5
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1answer
154 views

Better aligner than bowtie2?

Bowtie2 is probably the most widely used aligner because of it's speed. Burrow-wheeler (BW) algorithms (including bwa) tend to ...
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0answers
36 views

Finding parameters to separate 2 genes

If I have dataset of genetic sequences of 2 genes performing different things: how can I separate them? I want to find underlying differences between the 2 classes and common things among the 2 ...
3
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1answer
32 views

Is there any tools that can generating FBA model from genome sequences or proteome sequences?

Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a flux balance analysis model out of them? What I was thinking is more like to ...
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2answers
235 views

What is cellranger doing in comparison to other methods?

I've recently started working with the 10X-Genomics platform with Illumina (MiSeq and HiSeq) for single-cell RNA-Seq. I've been recommended the "cellranger" (version 2.1.0) which I understand handles ...
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0answers
61 views

How to predict the distance between two residues in a protein sequence

I have some protein sequences and I need to predict the physical distance between each two residues in the protein when folded correctly in 3 dimensions; I need to predict this distances just by ...
2
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1answer
62 views

SNP data Download Help

I am new to the field of Bioinformatics. Single Nucleotide Polymorphism or SNP data are available on the the Internet to download.SNP related data are valuable for variety of reasons ranging from ...
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1answer
37 views

Error while Importing fastq sequences to jMHC software

I am trying to analyze my .fastq files (MiSeq exon reads) with the jMHC software, but output files I have obtained have no results. I think I might be doing something wrong during the first step: "...
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2answers
171 views

Books on bioinformatics algorithms

I'm looking for a book about bioinformatics algorithms, such as alignment, BLAST search, and variant calling. I'm hoping reading about this subject will give me a deeper understanding of the ...
1
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1answer
111 views

Combine Fastq by writeFastq is not working properly

Currently I have 4 fastq file for each patient as WES data. For WES pipeline, I want to combine those fastq files. I am using writeFastq from ShortRead package in Bioconductor.But I think this ...
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0answers
18 views

How to use DCA to deduce the contacts between 2 proteins ensembles?

I would like to use DCA (direct coupling analysis) to analyze the interface between 2 protein ensembles (how the 2 ensembles interacts). Do you have access to a tutorial on this matter? A source code? ...
0
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1answer
42 views

What is the --rev_comp_mapping_barcode parameter in the QIIME1 script extract_barcodes.py?

I'm using the QIIME1 scripts extract_barcodes.py to extract barcodes from a dual-indexed MiSeq library, and then demultiplex my reads using split_libraries_fastq.py. I have been having trouble ...
4
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7answers
338 views

calculating nucleotide frequency per column

I have some sequences shown below ...
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0answers
36 views

How to rebuild the workflow for mining in oomynete genomes in UGENE

I want to recreate the UGENE workflow proposed in Convergence of retrotransposons in oomycetes and plants. After being able to understand the data and hmmsearch Here and Here and getting most of the ...
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1answer
87 views

Mini-bulk RNA-seq and scRNA-seq analysis differences?

We have RNA-seq data from libraries prepared using the Smartseq2 single-cell protocol on 500 cells (mini-bulk) / library. The complexity is much better than with single-cells (~14k genes for 1.5M ...
2
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2answers
53 views

Identifying relevant SNPs from a list

I have a list of all SNPs (a list of RsIDs) that fall in the coding sequence of several thousand human genes, and I'm looking for a convenient method to come up with a list of known SNPs that alter an ...
7
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3answers
529 views

Least present k-mers in the human genome

What are the least present k-mers in the human genome at different sizes? Starting with k=4 and going up in size until k=10, what are the k-mers least seen (or not at all) in the human genome? I am ...
2
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3answers
406 views

Filter BAM file for read pairs where one or both of the reads starts with a given sequence pattern

What's the most straightforward way to filter a BAM file for read pairs where one or both of the reads starts with a given sequence pattern? Would a tool that deals with UMIs work for this? Which one ...
0
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2answers
207 views

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 ...
2
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2answers
156 views

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 ...
4
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2answers
702 views

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 ...
4
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1answer
176 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
188 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. ...
4
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1answer
170 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, ...
1
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1answer
58 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
259 views

How does blastn sort output?

I used blastn to search one a genome database for the sequences in a file. ...
12
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3answers
152 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 ...