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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16 views

Calculating sequence divergence score for a protein from identity or similarity score?

I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue ...
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85 views

What does genetically tractable strain mean?

I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this ...
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42 views

Using BLAST for molecular replacement in structural biology

This is my first time trying to do molecular replacement to solve a protein structure. I am using the NCBI blastp program to find suitable search models. When choosing a search model, I understand ...
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41 views

Expected number of mismatches between two alleles of a gene in a population?

I can't find any article about the expected number of mismatches in alignment of two alleles of an assumed gene. Any reference or information about allele mismatch ratio (in a species or higher taxa) ...
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48 views

Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in ...
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47 views

in order to align genome multi-fasta files, do you ignore the chromosome sections?

I want to test my implementation of Needleman-Wunsch on two fasta files downloaded from https://hgdownload.soe.ucsc.edu/. However, fasta files on this site are multi-fasta and therefore are split into ...
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34 views

Available Protein sequence alignment dataset and HMM model

I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to generate noisy copies of the consensus sequence ...
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61 views

Different BLOSUM matrices [duplicate]

What is the difference between different variants of BLOSUM matrices? e.g What is the difference between BLOSUM 30 and BLOSUM 62?
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3answers
176 views

What tool can I use to align multiple protein sequences to one reference sequence?

I have a protein of interest which is ~300 amino acids in length. I also have around 40 short sequences (all 9 amino acids in length); these are all very different from each other. I would like to ...
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61 views

How to reduce the number of sequences in a Multiple Sequence Alignment?

I have a Multiple Sequence Alignment, where there are around 5000 sequences. There also exists many sequences where, there are so much of non-sequenced regions (for instance, AU----CGGGCA--NNNNNNNNNN)....
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303 views

How to interpret different results from Clustal Omega and Multalin?

I have been working on aptamers, which are nucleotide sequences. They bind to various targets, in my case a particular cell surface receptor. The people associated with the project performed SELEX and ...
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1answer
56 views

How evolutionarily conserved are UTRs?

Coding sequences of genes have a certain degree of evolutionary conservation, so that comparisons based on sequences (BLAST, HMMER etc) can be informative. Generally speaking, the more two species are ...
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42 views

Which database has the ready made 16S rRNA Multiple Sequence Alignment File that I can download directly from?

In my case, I need the ready made 16S rRNA Multiple Sequence Alignment File for E.coli and use it to generate the phylogenetic tree file in Newick format. I've tried using the one from utexas website, ...
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49 views

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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90 views

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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1answer
46 views

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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436 views

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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693 views

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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236 views

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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1answer
93 views

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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336 views

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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2answers
510 views

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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329 views

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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407 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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377 views

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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38 views

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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857 views

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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432 views

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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8k views

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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56 views

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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69 views

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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506 views

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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735 views

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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58 views

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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69 views

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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3k views

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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1answer
10k 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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1answer
164 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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345 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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278 views

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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1answer
2k views

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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1answer
609 views

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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460 views

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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915 views

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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22 views

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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95 views

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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161 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 ...