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.

Filter by
Sorted by
Tagged with
-2
votes
1answer
149 views

Algorithmic investigation of viral proteins for vaccine design [closed]

I wish to investigate how a virus could be attenuated through targeted mutagenesis by a priori prediction of attenuating amino acid mutations. In particular, I am seeking bioinformatic solutions where ...
1
vote
0answers
35 views

Given a multiple sequence alignment, how do I output all of the non-consensus characters by location?

I have an MSA from MAFFT (as a FASTA file; there are several sequences in the MSA), and I would like to quantify the "variants" between these sequences. What is the standard tool to do ...
2
votes
1answer
49 views

Sequence alignment of extended IUPAC sequences

I want to align a short sequence to a reference, and both are encoded in the extended IUPAC notation (i.e. 16 letters). What alignment software can I use for that? For example, in Bowtie "all non-A/...
1
vote
4answers
77 views

Tools for comparing/visualizing FASTAs?

I have two FASTAs/assemblies of the same species, but the bases are somewhat different. I would like to explore this. What tools/methods exist to compare two FASTAs and see the difference in ...
1
vote
0answers
18 views

How can I find genes of fundamental metabolic processes for an organism?

I want to find genes of fundamental metabolic processes in the Phytophthora cinnamomi genome. I'm using the genome sequence deposited in the NCBI and I'm searching ORF by ORF, using the ORF finder (...
10
votes
3answers
2k views

A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

Quote: We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have ...
4
votes
1answer
459 views

Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?

This is the BLAST tree of the latest coronavirus out of China (from Wuhan Institute of Virology, China). It seems strange that there is so much divergence from all the other coronaviruses. Is this ...
5
votes
1answer
845 views

Ancestry of the coronavirus 2019-nCov, WuHan city, China

In one of the answers to another question about the corona virus a link was given to this phylogenetic analysis of the virus. Can somebody assist a non-bio type here? It seems to show that the ...
164
votes
4answers
90k views

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it... ...
3
votes
2answers
147 views

What is the meaning of the "*" character in bwa fastmap's output?

I am mapping kmers back to a few bacterial genomes using bwa fastmap: ...
2
votes
1answer
150 views

How can I not show insertions in the Integrative Genome Viewer (IGV)?

I am using IGV 2.5.2 and would not like to see the insertions in my aligned reads. How can I do that? I have managed to remove mismatched bases because there is an option to do so when I right-click ...
8
votes
2answers
1k views

What is 'k' in sequencing?

When a DNA sequence is sequenced, I've only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a 'k' recently and I had asked another researcher who gave me an ...
1
vote
1answer
34 views

Finding simple sequence from reads with significant overlap

I wrote a "script" to pull out reads from a huge fastq file in an iterative manner, by finding homology to the previous sequence. It should be relatively easy to overlap them and assemble ...
4
votes
1answer
64 views

Is there a modern alignment tool tailored for transmembrane regions?

I am looking for a project or tool that allows programmatic pairwise alignments of proteins but that takes care with transmembrane regions of proteins. TM regions are traditionally too information ...
2
votes
1answer
1k views

how to calculate Pairwise Alignment Scores for blosum62

I have a bioinformatics exam coming up. I can understand the difference between the global algorithm and the local algorithm, but I have a problem with gap opening penalty and gap extension penalty. ...
2
votes
1answer
190 views

What do the symbols mean in minimap2's gap cost equation?

Heng Li's paper on minimap2 is understandable to me right up until the moment that it gives this definition of gap cost: 2.2.1 Alignment with 2-piece affine gap cost Minimap2 performs DP-based ...
2
votes
2answers
93 views

Is there any way to align ChIP-seq reads to telomeres?

I know that telomeres are highly repeated sequences, but is there any way to retain any reads that map to these regions (on HG38)? I recently managed to find some protein binding to centromeres, ...
1
vote
2answers
296 views

Smith-Waterman Pairwise Local Alignment Algorithm

I have written a R code for Smith-Waterman (SW) algorithm. I wanted to check the results of my code with online examples. In all cases -except one- I found the same alignment. So there is this one ...
1
vote
2answers
363 views

How to define an outgroup to build a robust amino acid tree

I building a robust amino acid phylogeny with adequate robustness support (see previous post here). This is a brief summary of what I have done: I performed a BLASTp analysis using a protein sequence ...
1
vote
1answer
122 views

Weird phylogenetic tree

I am required to create a phylogenetic tree(s) of my genes of interest and am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding my search. ...
1
vote
1answer
75 views

Best way to "fish" long reads that match a query sequence

Very simple set-up: We have a PacBio long high-fidelity (HiFi) reads, genome sequencing, and some of those that contain a particular sequence. I want to find out which ones. The length of the query ...
0
votes
2answers
108 views

Inferring a phylogenetic tree from BLASTn

I am trying to infer a phylogenetic tree from a Blastn output and from what I have understood, what I should do is 1) extract the alignments and re-align them using Muscle, then 2) feed the .aln file ...
1
vote
0answers
24 views

How to get a tabular summary from srspair alignment file?

I checked EMBOSS but there is no tabular output for pairwise alignment. I can write a script but would like to know if there is already a tool to summarize an alignment in srspair format in the form ...
0
votes
1answer
79 views

How to reproduce this specific sequence logo from 10 000 human mRNAs?

this is A sequence logo showing the most conserved bases around the initiation codon from 10000 human mRNAs. I would like to reproduce this sequence logo. How can I get the sequences? which database ...
0
votes
0answers
31 views

BLAST server download

I discovered that Phytozome's BLAST results look quite nice (please see below). By any chance, does anyone know where to download this BLAST server in order to install it locally for organisms which ...
1
vote
1answer
74 views

what does a sequence look like before alignment?

I am confused with Sequence alignment, which is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, ...
1
vote
1answer
833 views

How to compute the Shannon entropy for a strand of DNA?

I'm confused by the computation of sequence logo. Wikipedia gives a process about this without a concrete example. Let's just consider DNA, so there are 4 bases (nucleic acids). The following data ...
2
votes
1answer
214 views

Why do ten rows (Figure_1) correspond to 2 bits (Figure_2) in a sequence logo?

Following this question, I'm confused with the computation of sequence logo Following data comes from the book "Machine Learning - A Probabilistic Perspective (Figure_1)" here is the corresponding ...
1
vote
1answer
378 views

What is "aligned sequences" and "consensus sequence" in the context of sequence logo? How to compute these?

In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). so, What is "aligned ...
3
votes
1answer
66 views

For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?

The genomes are from same species. Is it true that, in phylogenetic tree constructed from amino-acid based MSA (multiple sequence alignment) some information are lost, so for phylogenetic ...
1
vote
2answers
369 views

Differences in webtool and standalone Clustal Omega Percent Identity Matrix

I'm trying to align sequences using MUSCLE in my own computer. To compute Percent Identity Matrix I'm trying to use Clustal2.1 like it's done in https://www.ebi.ac.uk/Tools/msa/muscle/. Even though I'...
0
votes
1answer
262 views

How to combine multiple files into one file?

I have multiple files (n=86000) with one column each and I want to combine them all into one file with 86000 columns. I tried the following command ...
3
votes
2answers
158 views

Produce a single sequential FASTA sequence out of BAM

I'm having problems properly looking for a solution because I'm a layman in Bioinformatics not familiar with the terminology. I'm hoping you can nudge me in the right direction, please! Thank you very ...
1
vote
2answers
75 views

Global or local alignment on sequences for which it is assumed that they have common ancestry

As the title says I would like to know which alignment method(global or local) should I use for sequences for which is assumed that they have common ancestry? The sequences are 21 aa long peptide ...
1
vote
1answer
221 views

A GTF annotation for GRCH375d version

I have been given a bunch of .bam files, that come from the alignment on GRCh37d5 of human genome by Star tool. I want to extract raw read counts from these bam files by FEATURECOUNTS tool so I need a ...
6
votes
1answer
88 views

Is there a way to assemble contigs starting from a specific sequence?

My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic ...
6
votes
2answers
537 views

Are phylogenetic tree construction algorithms any different than general clustering algorithms?

Are phylogenetic tree construction algorithms any different from clustering algorhithms? I suspect the answer is no. Of course phylogenetic tree construction uses biological knowledge, e.g special ...
0
votes
1answer
64 views

How to find the position-specific weight matrix (PSWM) for a list of genes having different sizes?

Wiki has the algorithm for finding position-specific weight matrix (PSWM) for a list of nucleotide sequences having an equal number of nucleotide. How do we find the PSSM for a list of nucleotide ...
4
votes
2answers
132 views

How to predict stop codons in Illumina reads?

I have Illumina MiSeq paired-end reads from 150bp amplicons mapped to my reference genome (> 1000X coverage). These reads have indels that may or may not induce frameshifts. If the indel induces a ...
3
votes
1answer
80 views

How to interpret UniProt allele patterns?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there ...
7
votes
2answers
2k views

Definition of "seed" in sequence alignment

I would like to know what is meant by "seed" for various sequence aligners. How is it important?
0
votes
1answer
12 views

Empty .result in MirDeep Star

I am using MirDeep star tool for RNA sequence alignment. I have tried both GUI version and command line version of this tool. But every time, I am getting empty . result file and .known_mir file. This ...
1
vote
0answers
342 views

Aligning nucleotide sequences in APE software

I am very new to APE software. I am trying to align complementary oligo-DNA strands using APE on macOS. I have both the forward and reverse sequence of an oligo-DNA insert in two separate files. But I ...
3
votes
3answers
237 views

Alignment with arbitrary number of mismatches or gaps

I have 23bp long reads and want to find all possible alignments of them to the human genome (hg19, hg38) for an arbitrary number of mismatches (<7), possibly also small indels. I've read in ...
5
votes
3answers
2k views

How to get fasta alignment file from SAM/BAM file?

I am not talking about consensus sequence, I know how to get consensus sequence using mpileup in samtools/bcftools. As I understand , SAM/BAM files are basically sequence alignment format so it's ...
5
votes
4answers
3k views

How to create Phylogenetic Trees from fasta files in Python or R?

I have around a hundred Fasta files (and will collect several thousand) with DNA sequences and +50x coverage. What is a recommended method to construct a phylogenetic tree? Solutions in Python or R ...
3
votes
1answer
108 views

How to quantify similarity of genomes and find differences in set of S aureus genomes?

I have around 500 annotated proteomes of different bacterial strains and would like to quantify their similarity (or difference). I found gt genomediff from ...
4
votes
1answer
671 views

Why do I get so many insertions from Minimap2 on my Nanopore WGS?

I'm a starting my analysis on nanopore whole genome sequencing. I start my analysis from this popular Github. The sample I downloaded was WGS for NA12878, so I would assume it's alignment to GRCh38 ...
3
votes
2answers
3k views

Python - Finding a motif - input: a txt file with 10 sequences and 10 motifs

When I run my BruteForce function with only one input it works and the result is correct. ...
5
votes
2answers
186 views

Calculate the percentage of each unique phylogenetic tree in a BEAST output

I have a nexus formatted BEAST output containing 20,000 phylogenetic trees of seven taxa. Is there any way to get the percentage of each unique phylogenetic tree contained in this output? I already ...