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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questions
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merging two/or more bed file into one bed file
I am trying to merge two bed files (more in future) to one. my bed files are something like :
.
I need to merge them in a way to have the shared chromosome location.
Is there a way to do that ?
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2answers
83 views
Understanding some of the computational bottlenecks of Covid-19 research
I am a researcher in high-performance computing (with very little bioinformatics background), and I am trying to understand what are the current biggest computational bottlenecks of softwares used for ...
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1answer
35 views
Overlap in Paired-end Reads for Sequencing?
Regarding Sequencing:
Do/can the paired-end reads have overlaps?
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1answer
43 views
Location of Reads in Sequencing
I have questions regarding sequencing:
Are paired-end reads from different stands?
What about single reads, are they coming from both strands?
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1answer
25 views
How to do BLASTP for short sequences (<20 aa) effectively?
I am trying to find sequence homology between viral sequences and my protein of interest. I have the sequences of their epitopes which varies from 5 to 500 amino acids long. For shorter sequences, it ...
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1answer
39 views
Identifying proteins in a concatenated protein sequences [closed]
I have a 120-concatenated protein sequence in a fasta file. I would like to split by proteins.
How can I identify each protein?
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26 views
Given a multiple sequence alignment, how do I output all of the non-consensus characters by location?
I have an MSA from MAFFT, and I would like to quantify the "variants" between these sequences.
What is the standard tool to do something like this?
I'm familiar with calculating an MSA, and then ...
2
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1answer
35 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/...
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3answers
48 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 ...
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16 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 (...
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1answer
56 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:
...
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1answer
40 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 ...
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1answer
17 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 seems like it should be relatively easy to overlap them and ...
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0answers
36 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 ...
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1answer
72 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
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1answer
49 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 ...
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2answers
76 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, ...
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2answers
66 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 ...
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1answer
59 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 ...
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2answers
45 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 ...
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0answers
16 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 ...
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1answer
75 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 ...
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0answers
30 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 ...
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1answer
58 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, ...
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1answer
315 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 ...
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1answer
101 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 ...
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1answer
180 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 ...
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1answer
55 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 ...
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0answers
108 views
How to get a MSA fasta from BAM/SAM?
I am working with paired end NGS miseq data from a viral genome with multiple timepoints. I have filtered and trimmed this data for quality and adapter sequences. I have then merged the filtered ...
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1answer
123 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'...
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votes
2answers
80 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 ...
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2answers
40 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 ...
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vote
1answer
133 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 ...
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1answer
81 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 ...
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1answer
31 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 ...
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2answers
107 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 ...
6
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2answers
771 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?
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1answer
11 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 ...
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0answers
201 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 ...
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3answers
121 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 ...
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3answers
1k 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 ...
4
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1answer
454 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 ...
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2answers
1k views
Hardware Requirements (specs) for Bioinformatics-dedicated desktop [closed]
I know this is a somewhat general or vague question, but I’m interested in your opinions. I must build a desktop for general bioinformatics activities with human genomes. I will work with Python and R ...
3
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1answer
63 views
Seeking explanation of the hg38 files downloaded from bowtie 2 website
I downloaded the H. sapiens, NCBI GRCh38 files from Bowtie's website. After unzipping, there are 6 files, 4 that end in set 1.ebwt, set2.ebwt, set3.ebwt, and set4.ebwt and two that end in set.rev.1....
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1answer
50 views
Restricting match output for multiple sequence alignment using mafft?
So I aligned roughly 5k sequences and I got my output using mafft. However, I want to restrict the output to only present conserved segments of a specific length (let's say 25bp). Does mafft have ...
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2answers
243 views
How to check if indels in VCF files are left or right aligned?
I downloaded a VCF file from dbSNP, and I'm curious if the indels in the file are left-aligned for GRCH37 genome. The documentation doesn't say anything.
How can we tell if a VCF file has left or ...
4
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1answer
195 views
Can blat use more than one core/CPU to speed up the alignment?
I am using BLAT to align two versions of the genome of C. elegans. I can see in the Activity Monitor of my Mac Book Pro High Sierra that blat is using 100% of a CPU....
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1answer
205 views
Proof of Breakpoint Reversal Sorting Approximation Algorithm
I'm kind of new to bioinformatics and trying to self-study. I'm reading a bioinformatics book: An Introduction to Bioinformatics Algorithms and ran into some problems about understanding the proof of ...
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6answers
535 views
Identifying Indels from Chromatograms
I have around 100 chromatograms (.ab1 files) from Sanger sequencing a genome at loci believed to have an indel.
I'm new to interpreting this kind of data in ...
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3answers
828 views
How BLOSUM Matrix is constructed and calculated
I would like to ask how BLOSUM matrix is constructed and calculated ? I read the wikipedia and I still do not understand it. I do not understand the mathematical calculations as I have low knowledge ...
