Questions tagged [sequence-alignment]

Use this tag to refer to the alignment of nucleotide or peptide sequences, producing an arrangement that maximizes similarity between sequences.

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What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve?

What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve? I am particularly interested in seeing the single nucleotide ...
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1answer
108 views

Coordinates to Genome R Studio Script?

I have a very, very long list of genome coordinates of areas. I need to gather a sequence in order to compare it to another database of sequences that I have. How do I produce the genome sequences ...
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2answers
1k views

How to align genomic sequence with corresponding amino acid sequence

Does anyone know of a program that can align a genomic sequence with introns with the corresponding amino acid sequence? I have both the genomic sequence and the correct amino acid sequence but no ...
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1answer
1k views

Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?

Disclaimer: This is a self answered question for documentation purpose and I adapted this from the following github gist. Especially from users terrycojones and peterjc as well as sujaikumar who ...
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1answer
1k views

What is local realignment and what is the problem it solves?

I am trying to understand local realignment but I could not get a clear idea of what is the problem solved by it. For example, reading Homer and Nelson (2010): Because alignment algorithms map ...
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1answer
232 views

Filtering out all seqs with mutations of list2 from list1

I have 2 lists, list1 and list2, of protein sequences of the same given gene in different strains. In ...
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2answers
425 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 ...
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1answer
57 views

Finding out proteins that have a similar domain to a specific toxin

I am trying to find out that which DNA sequences(in the below) have a similar domain to a specific toxin which is Clostridium botulinum You can find the fragment of the DNA sequence that belong to ...
2
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1answer
380 views

Mark BWA-SW split alignments in output for long reads

Is there a way to remove split alignments of single-end long reads from BWA-SW output? BWA-MEM has an option to include or flag split alignments in the result, but it seems BWA-SW method include them ...
2
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1answer
738 views

Counting number of possible alignments between two DNA sequences using python

I was looking BioPython to calculate the number of possible alignments between two sequences. Let's say there are two input sequences with the length of m and n. The program will count the possible ...
5
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3answers
640 views

How can I only get the species name for fasta sequences from blast results?

I am trying to make a phylogenetic tree from sequences obtained with blast. I have files that contains hundreds of fasta protein sequences which are all named like ...
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2answers
115 views

Uniprot: Determining protein and organism given a DNA sequence

I would like to find the identity of a protein, together with the organism name and kingdom. The given DNA sequence is below: ...
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2answers
872 views

Waterman-Smith-Beyer Sequence Alignment

I am having trouble understanding the affine gap penalty in the following example - I am not sure where the 3 and 4 come from or the 4 and 5 in cells 1,3 and 2,4. I'm not understanding how the affine ...
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1answer
68 views

TCGA bam file duplicates (aligned reads) and related last part of TCGA barcode

I am running an analysis on TCGA bam files (GCRh37/hg19) of whole exome sequencing data. I usually find one bam file for each sample. However, at least one sample has two bam files, in which the last ...
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2answers
303 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 ...
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2answers
8k views

Meaning of BWA-MEM MAPQ scores

Does anyone know what the MAPQ values produced by BWA-MEM mean? I'm looking for something similar to what Keith Bradnam ...
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1answer
38 views

Identity plus Similarity Interpretation

I am helping a colleague to interpret protein multiple sequence alignment results. My colleague used a third-party proprietary solution (I know...) to calculate the alignment, and one of the resulting ...
5
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1answer
548 views

Multiple sequence alignment with R [closed]

I want to incorporate Multiple sequence alignment into our Shiny app, i.e. allow the possibility of selecting different nucleotide sequences, and do a multiple sequence alignment in real-time. The ...
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1answer
183 views

Profile of conservation between bacterial sequences and human protein

My goal is to make a conservation plot between bacterial sequences and a human protein. So far, I have a FASTA file of the protein, and a FASTA file with the sequences of the proteins from the BLAST ...
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3answers
2k views

Which sequence alignment tools support codon alignment?

Sometimes it useful to perform a nucleotide protein coding gene sequence alignment based on codons, not on individual nucleotides. For example for further codon model analysis it is important to have ...

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