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Questions tagged [sequence-alignment]

A computational technique to compare two nucleotide or protein sequences. There are two basic types of sequence alignment i.e. local alignment (local comparison of subsequences) or global alignment (end to end comparison of the entire sequences).

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Sequencing inaccurate at the primer site

The times I have sent a sample to sequence, both the forward and the reverse primer sites, show high inaccuracy while the rest of the gene is correctly sequenced. Because of this, the sequences of my ...
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Consensus symbols in multiple sequence alignment [closed]

I was using multAlin for multiple aligning a set of sequences. The output I and came across included the following documentation (English corrected): Consensus symbols: ! is any of IV $ is any ...
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Confusion about a gene's description

I have a very basic biology question. I am reading the description of gene FAM166A here, and I have no idea what "sequence similarity 166" means. What does 166 stand for, what is this gene's sequence "...
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Progressive Multiple Sequence Alignment: “Add” a sequence to the MSA

I understand the basic steps of progressive sequence alignment: Construct a pairwise distance matrix between all sequences Based on that, construct a guide tree Pick the closest two sequences from ...
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Better algorithm than Burrow-Wheeler, for aligning short reads with high number of mismatches

Burrow-wheeler (BW) algorithm is probably the most widely used aligner out there. Largely it is popular because of it's speed and tendency to not take much memory. However, it has limitations when it ...
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How to pipe Bwa-mem output without saving SAM file

I'm trying to find circular ARN using the program CIRI2. CIRI2 takes as input SAM file from BWA-mem, but I would like to go straight to CIRI2 output without saving SAM file. Is there a way to achieve ...
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Details of Needleman–Wunsch algorithm

I try to understand details of the Needleman–Wunsch algorithm and use an example from the book [Nello Cristianini, Matthew W. Hahn. Introduction to Computational Genomics. A Case Studies Approach, www....
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Maximum Parsimony Multiple Sequence Alignment

I have one question that I find awfully confusing to follow. Maximum Parsimony Multiple Alignment Problem Given: A set of sequence S1,…,Sn, and a tree T with one leaf per sequence Find: The ...
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347 views

How does Blast algorithm actually work?

I tried Googling for hours and am still not sure how it works. As far as my knowledge goes, this is what Blast algorithm does: Goal: Given a query Q and a pre-processed DNA sequence D, return all ...
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What is the difference between contig- and read-based sequence alignment?

I am trying to understand the difference between read based and contig based alignment. Is contig based alignment refer to de novo assembly and then it is align to a reference genome. I am confused ...
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How to convert bwa mem output to BAM format without saving SAM file

I want to go straight from bwa mem alignment to BAM format as I don't need the SAM file and it takes up too much space. How do I achieve this?
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Webtool to design guide RNA (gRNA) for use with CRISPR-AsCpf1?

My goals are to use a free webtool to: Identify guide RNAs (direct-repeat sequence followed by the targeting sequence) appropriate for use with AsCpf1 in order to target a specific segment of genomic ...
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What is the best alignment definition for the Multiple Sequence Alignment (MSA) problem?

For simplicity, suppose that I am penalising mismatches and gaps with -1 and adding a score +100 for each match. Does the optimum alignment of the three DNA sequences ...
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What does chrUn mean in the output from a Bowtie run on human sequences?

After having performed an alignment using bowtie2 and GRCh38 as a reference sequence, I got inusual matches on chrUn. Here a small part of the SAM file: ...
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Is setting high mismatch and gap penalties sufficient to distinguish perfectly mapping reads?

I have a fat pile of 125bp whole genome shotgun reads that have undergone quality control, and I would like to pull out just those reads that do not map perfectly to the genome. When I set extremely ...
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299 views

How to detect Single Nucleotide Variants (SNVs)?

This image is obtained from this paper. The description of this image is as follows:- DNA-sequence reads from a tumor sample are aligned to a reference genome (shown in gray). Single-nucleotide ...
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Designing degenerate primers using alignment of protein sequences from other species

I am trying to design a PCR primer for a gene whose sequence is not known. Even the whole transcriptome sequencing done in our lab did not identify that particular gene. Hence, I guess I am left with ...
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Creating BLAST database with nucleotide “place holder”

I have a set of nucleotide sequences that contain some special characters with multiple meanings: H -> C, A or T K -> G or T M -> C or A R -> G or A S -> C or G W -> A or T Y -> c or T I would like ...
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What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?)

Both HMMER and BLAST report an e value for alignments. Is it calculated in the same way and - assuming that default settings are used - can they be compared directly (are the equivalent)? If not ...
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Identity and similarity for Multiple Sequence Alignment (MSA) of proteins

I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am ...
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What is the meaning of “E-value” in the BLAST search?

After reading many pages, I still do not understand the definition. Can someone use simple words to explain me that? https://en.wikipedia.org/wiki/BLAST This expectation or expect value "E" (often ...
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Are there any examples of weighted edit distance genome alignments?

It has been said that weighted edit distance is a preferred way to compare/align genomes in practice, e.g., when identifying genetically similar patients. I wonder if there are some concrete examples ...
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What factors should I consider when selecting a reference genome for mapping?

I am under the impression that the most recent reference genome is typically the best case. What other things should I consider when selecting a reference genome? For example, is there any particular ...
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What is a good multiple alignment of large genome sequences when working with limited hardware?

I need to align bacterial genomes (namely mycobacteria, over 4 Mb in length), and my choice would have been either 'muscle' or 'clustalW'; however these algorithms are too memory demanding for such ...
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Phylogenetic tree with tagging

I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the ...
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Do all multiple sequence alignments employ global alignment algorithms?

Multiple sequence alignments are usually done between sequences of similar length, which resembles best a global alignment. However, I'm not sure at all what the algorithmic background would be in ...
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Finding diploid neanderthal alignment data, looking for ambiguity codes

I'm using Neanderthal alignment data from here: http://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html Specifically, the .bam files. I would like to find alignments for neanderthal ...
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How does one apply Bayesian inference to quantify a read the deeper you sequence?

For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule. What is the ...
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Why does BLAST reduce word size for short proteins?

I'm using BLAST to identify a short protein (BLASTp). If I check the short query then the word size reduces from 3 to 2. However the search will then be less ...
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5k views

How to interpret Percent identity matrix created by Clustal Omega?

I did a multiple sequence alignment using Clustal omega. checked similarity for 3 protein sequences : aspartyl aminopeptidase [Homo sapiens], aminopeptidase P (APP) [Plasmodium falciparum 3D7], yeast ...
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103 views

why does the score matrix influence the E value (BLAST)

When I align two HBB protein sequences wich have 80% identity, I used two kind of score matrices: Blosum62 and PAM30, to figure out the impact on my results. I noticed that the bit score is higher ...
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271 views

How to compare Smith–Waterman algorithm implementations?

Assume that you have two implementations of the Smith–Waterman algorithm (with what ever heuristic they apply to speed up) for local sequence alignment of genomic sequences. I would like to know if ...
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Difference of coverage between amplicons

I have 2 fastq files and I generated BAM file (indexed and sorted) of some reads. I aligned them to a reference genome (hg19). I am working with different primers. ...
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What are unmapped reads?

I am mapping some reads to a reference genome (hg19). I used bamtools to have the percentage of mapped vs unmapped reads. ...
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constitution of read and gene region (IGV)

I work with fastq files containing NGS reads for some human DNA regions. The reference genome is hg19. I had two fastq files (pair-ended). I generated alignment BAM files. I used "bwa" and samtools to ...
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What tool to use to map reads (samtools, sequencher,…)?

I am a beginner in Bioinformatics. I have 4 files: 2 fastq files (aln1.fastq and aln2.fastq) 2 bam files (aln.bam and aln.bam.bai) I know that: the raw file is aligned to hg19 human genome. The ...
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Question about SAM CIGAR string

My question is about the CIGAR specification. The documentation states: M 0 alignment match (can be a sequence match or mismatch) ...
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How to search for a protein sequence of an specific taxa in NCBI?

My example: Sequence of HBB (Hemoglobin Beta) in Fishes. How can I do a good search to obtain above sequences in NCBI? (I know hot to download them into a FASTA file)
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Do the BLAST scores have any relation between them?

Is there any relation among the BLAST scores (E-value, similarity, identity, gap, bit score)? Is the e-value score for an alignment proportional to other scores, such as similarity score (i.e. the ...
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132 views

How is the probability of a sequence occuring with BLAST calculated?

What is the probability that a given nucleotide/amino acid sequence will occur in the whole database program BLAST searches in? How this probability is calculated?
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Blosum matrix computation with X%

Why does the answers to the problem found in the referenced pdf, differ from my calculation below? I am trying to understand the math from this pdf from an online tutorial I am reading and my own math ...
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In DNA sequencing, is “mate pairs” synonymous with “paired ends”? If not, how do they differ?

By just looking at Roach et al's paper I get the impression that they are the same thing, and the Wikipedia URL for the former is a redirect to the latter. However, I suspect they are not exactly the ...
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How is output of DNA assembler measured?

I developed own DNA assembly pipeline. Input is set of reads and output is set of contigs. Many papers measure own algorithms and compare it against each other. There are basic metrics like: N50, N70....
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How to Determine the Most Conserved Sequence from BLAST Result?

I used BLAST to find the best aligned DNA sequence to my query sequence. The BLAST result shows a number of sequences that it calculated to be the best aligned sequences to the query sequence that I ...
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How do I run each individual record in a multi-fasta file against a database using PSI-Blast?

I'm new to standalone blast+ and the linux terminal. I set the bash-profile to load the PATH and BLASTDB for my blast already, but I don't know how to use psi-blast yet. How can I do the search ...
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What is the difference between sequence alignment and sequence assembly?

I read the wikipedia page about sequence alignment and sequence assembly but I have not been able to find any difference between the two. What is the difference between sequence alignment and sequence ...
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780 views

How to do multiple sequence alignment?

I have a DNA sequence that makes protein 1. but now I have asked to: compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi sequence alignment (MSA) of the ...
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Do the bacterial species X, Y, Z code for proteins A, B, C?

My PI has assigned me a task to gather evidence to determine whether or not a list of particular species of Campylobacter and Helicobacter code for a list of several proteins. To put it simply I’ve ...
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blastn: What substitution matrix is used?

I'm currently working aligning sequences, and I need to compute similarity between pairs of DNA 'words' of a particular length. For amino acids I am able to use the substitution matrices in Biopython ...
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Determining the percentage of the query of an alignment from a BLAST output

Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that ...