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).

Filter by
Sorted by
Tagged with
0 votes
1 answer
66 views

How to calculate the conservation score of specific amino-acids or motifs in a multiple sequence alignment?

The proteins I'm interested in create disulfide bonds using cysteine pairs. In different states of the proteins, those pairs are sometimes formed, other times they stay separated. I would like to ...
Assa Yeroslaviz's user avatar
2 votes
1 answer
95 views

MSA cluster and MSA depth

I was reading the AlphaFold paper and had difficulty with a couple of terms introduced in the main text of the paper. I asked ChatGPT what these were but I'm not sure that it's accurate. I had a hard ...
Jack's user avatar
  • 21
0 votes
1 answer
63 views

Sequence identity and coverage in multiple sequence alignment of proteins

This might be naive since I am very new to the field, but I wonder about the difference between sequence identity and coverage in multiple sequence alignment of proteins. I imagine the calculation ...
Jack's user avatar
  • 21
3 votes
1 answer
170 views

Can somebody explain why mouse and cow are the least related based on this sequenece alignment?

Answer key says out of the choices, the mouse and cow and the least related. Is it because they have the most number of differences out of the four choices? (Hedgehog/Horse is 5, dog/horse is 3, mouse/...
geneticscodingnoob's user avatar
3 votes
0 answers
206 views

Aligning two PDB structures with different numbers of atoms

What options do I have to align two PDB-files of ribosomes but with different number of atoms? I need to do the alignment using selection "name CA or name P", because the ribosome has both ...
HungryMolecule's user avatar
0 votes
1 answer
160 views

Alignment given two sequence

I have two sequences and I need to perform sequence alignment to determine all possible sequence alignments. I have created the matrix and managed to find 16 alignments. I wanted to understand if I ...
Krellex's user avatar
  • 101
-1 votes
1 answer
125 views

How to align more than 2 sequences with Needleman-Wunsch?

I have a DNA sequence of a protein and around 1200 zinc finger target sequences. These zinc finger target sequences are 9 bp long, resulting in BLASTn not finding them in the sequence. Needleman-...
honhon's user avatar
  • 3
0 votes
0 answers
44 views

Is it OK to use predicted protein sequences from RefSeq for protein sequence alignment?

I'm doing a project, and my goal is to do alignments of a particular gene product to see if there is any conservation of secondary structures across different species. So far, I have found a few from ...
help needed's user avatar
0 votes
1 answer
163 views

What is limiting the accuracy of genome sequencing today?

What are the current limiting factors of genome sequencing accuracy? By accuracy I mean a closeness relation between the sequenced genome and the finally assembled (I am not sure whether there is a ...
Frank Hauser's user avatar
2 votes
1 answer
125 views

What is the relationship between a "main" strain genome and its variant genome in archaea?

I am going to analyze DNA sequencing data in order to try to extrapolate some information about the survival strategy of Pyrococcus Furiosus to gamma irradiation, as maybe you already know from all ...
Manuela's user avatar
  • 443
1 vote
1 answer
86 views

What is the typical arrangement of amplified genes in archaea genome?

I have to check if some genes are amplified with bioinformatics tools, but, in order to do it, I need to know what this means from a biological point of view. It seems not so difficult to understand, ...
Manuela's user avatar
  • 443
1 vote
1 answer
196 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 ...
user345394's user avatar
3 votes
1 answer
1k 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 ...
Manuela's user avatar
  • 443
3 votes
1 answer
59 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 ...
lighthouse's user avatar
-1 votes
1 answer
82 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) ...
MySky's user avatar
  • 2,264
3 votes
1 answer
52 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 ...
alimm94's user avatar
  • 31
0 votes
1 answer
110 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 ...
Aly Shmahell's user avatar
-1 votes
1 answer
86 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 ...
Qinsheng Zhang's user avatar
-1 votes
1 answer
607 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?
HBashanaE's user avatar
1 vote
3 answers
746 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 ...
agatha's user avatar
  • 11
1 vote
2 answers
208 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)....
User's user avatar
  • 143
1 vote
0 answers
792 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 ...
Abhishek Bastiray's user avatar
2 votes
1 answer
63 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 ...
LinuxBlanket's user avatar
  • 1,313
0 votes
0 answers
67 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, ...
User's user avatar
  • 143
1 vote
1 answer
59 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 ...
Franco Grosso's user avatar
1 vote
1 answer
155 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 ...
Skyd4ncer's user avatar
2 votes
1 answer
57 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 "...
user5054's user avatar
  • 393
2 votes
1 answer
646 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 ...
Leonor's user avatar
  • 21
4 votes
1 answer
960 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....
Konstantin's user avatar
1 vote
1 answer
290 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 ...
Sarah's user avatar
  • 13
13 votes
2 answers
25k views

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?
Michael Hall's user avatar
3 votes
1 answer
109 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 ...
Jayden.Cameron's user avatar
-1 votes
1 answer
408 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 ...
mercury0114's user avatar
2 votes
2 answers
803 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: ...
alec_djinn's user avatar
  • 3,098
1 vote
2 answers
523 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 ...
Daniel Standage's user avatar
1 vote
2 answers
473 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 ...
Sayantan's user avatar
0 votes
1 answer
444 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 ...
kash91's user avatar
  • 91
1 vote
0 answers
52 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 ...
JanDotNet's user avatar
  • 111
2 votes
2 answers
1k 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 ...
nano's user avatar
  • 21
0 votes
1 answer
585 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 ...
wrong_path's user avatar
6 votes
1 answer
10k 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 ...
lanselibai's user avatar
2 votes
0 answers
59 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 ...
haskell looks great's user avatar
0 votes
1 answer
87 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 ...
Sebastian Lobentanzer's user avatar
1 vote
2 answers
620 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 ...
Gigiux's user avatar
  • 547
2 votes
0 answers
70 views

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 ...
Sceada's user avatar
  • 121
1 vote
3 answers
1k 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 ...
oaklander114's user avatar
2 votes
0 answers
62 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 ...
ghgh's user avatar
  • 75
2 votes
0 answers
71 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 ...
ShanZhengYang's user avatar
3 votes
1 answer
4k 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 ...
KingBoomie's user avatar
  • 2,380
1 vote
1 answer
16k 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 ...
Ak2817's user avatar
  • 391