Questions tagged [alignment]

These questions are about sequence alignment.

29 questions with no upvoted or accepted answers
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1answer
161 views

Chimera Alignments

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want ...
4
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1answer
61 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 ...
4
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0answers
124 views

convert supplementary reads to primary in sam or bam

I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names ...
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0answers
41 views

RNASeq read coverage in protein space?

I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly. I have also conducted a multiple sequence ...
3
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0answers
101 views

How to assign the best gap penalty and gap extension penalty using BLOSUM65

For an assignment I must do a pairwise optimal local alignment using BLOSUM65 and five protein sequences. The algorithm I want to use is the Smith-Waterman. Context protein sequencing using Blastp: ...
3
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0answers
57 views

Trying to show the gaps of each seq on bio::Graphics after converting clustalw

I've been having trouble for a while with this and have been trying to get this on my own, but I can't. I'm trying to display the gaps using Bio::Graphics after ...
3
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0answers
151 views

R Biostrings pairwiseAlignment to BAM

The R package Biostrings has a function to create a pairwiseAlignment from pattern and subject sequences. So far I can save the result into a text file using writePairwiseAlignments. I would like to ...
2
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0answers
31 views

Alignment using secondary and tertiary features of DNA

I m trying to align different sequences of length not greater than 50 bp. Could I incorporate additional information such as stacking energy, entropy, bonds etc as additional criteria in the alignment?...
2
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0answers
101 views

aligner for 1D^2 oxford nanopore data

I am wondering if anyone has tried aligning 1d^2 RNA-seq data. I am trying that on minimap2. It is giving me very low ~50% of mapped reads. it gives ~95% mapped reads for 1D. I am using the following ...
1
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0answers
31 views

BAM file filteing to remain best isoform

I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. After the BAM filtering steps, I used the Scallop results with TransDecoder....
1
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0answers
23 views

What are the symbols of $*$ and '$\_$' in an unknown alignment format for HLA data from the IMGT dataset?

Has anyone worked with the IMGT HLA database/dataset before? IMGT-HLA git repo they have some convenient text files (eg. link to gene A .txt file) with the genomic data for the different alleles of ...
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0answers
80 views

How can I interpret multiple alignment results?

I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE. I would like to ask if consistency score plays any role in the interpretation? I ...
1
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0answers
36 views

Unmapping Alternative reads in BAM file

I want to do some HLA typing, most of the tools require the bam file is aligned to primary genome without alternative read handling. From the International Genome Sample Resource project, I can get ...
1
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0answers
182 views

bedtools coverage - Report the depth at each position in each A feature

I am using bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected. Instead it reported 0 coverage at every positions. This is how I did ...
1
vote
1answer
151 views

Read alignment using Bowtie2

So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided to use their datasets. The ...
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0answers
327 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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0answers
13 views

Finding the conserved region of protein in a given set of Kingdom

We have to find the conserved region of proteins in a given set of kingdom and we have to give more weightage to distantly related organism. What approach I should take to solve this problem?
1
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0answers
28 views

Stand alone chaining tool for existing blast hits?

I have a table of blast hits in a database that I'd like to chain. What is a good choice for a 'stand alone' chaining tool? Is it simple to implement in Perl, for example? Example 'hit' data is here. ...
1
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0answers
39 views

How can I determine a mean sequence divergence for 10k sequences?

I am trying to analyze a number of repetitive sequences and as one step want to calculate a sequence divergence between the elements I found. Now in theory I wanted to generate a MSA of the sequences ...
1
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0answers
80 views

Mugsy error: Can't find species II dna at output/software/mugsy_x86-64-v1r2.3/mugsy line 501

I have installed mugsy in order to create a multiple genome alignment and a phylogenetic tree of several species of nematodes. The following command successfully pulls out the help: ...
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0answers
151 views

igv_plotter error: Xvfb did not start

I am trying to get screenshots from alignments of reads to a genome in IGV (Integrated Genome Viewer) using igv_plotter. ...
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0answers
130 views

Can Mauve export indels or is there an whole-genome aligner that can export indels?

I have aligned two whole genomes of the same species in Mauve using progressiveMauve. One of the genomes is 2 megabases longer than the other so I know it must contain some insertions. Looking at the ...
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78 views

STAR aligner multiple fastq files

I’m using STAR to align fastq files from SMART-seq2. I have raw data folder containing sub-folders with samples names the sub-folders each contain fastq file. How can I make a bash command in order ...
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0answers
6 views

Mutated residue number shown wrong in foldX yasara

I am trying to mutate phenylalanine 274 position in Uracil DNA glycosylase with alanine. The pDB file has the protein starting from 82nd residue. After the repair the console shows FA161A. The residue ...
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0answers
28 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 ...
0
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1answer
58 views

How to change sequence format in my alignment file?

I have fasta file with alingned several sequences (from MUSCLE), when I open it (e.g. notepad++) they look like: And I want dot format of identities like and then save it in txt file. I failed ...
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32 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 ...
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25 views

How to build ML tree among OTUs and 16s sequence

I have OTUs sequence generated from 16s V4 clean reads, and want to build maximum likelhood tree with selcted taxonomy 16s refseq from Sliva database. ...
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0answers
87 views

How should I deal with segmental duplications when aligning NGS reads to a reference genome?

This is a follow-up of my other question. I have been having trouble calling variants in the human SMN1 and SMN2 genes, because the human genome has a large segmental duplication there and these two ...