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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1answer
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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 ...
5
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1answer
69 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 ...
0
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1answer
19 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 ...
3
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1answer
68 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
85 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
10 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
51 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
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3answers
71 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 ...
4
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1answer
216 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
212 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 ...
2
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2answers
110 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
17 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
26 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 ...
7
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2answers
75 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
135 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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0answers
67 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 ...
5
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5answers
160 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
145 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 ...
5
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1answer
114 views
Understanding the initialization of the Needleman-Wunsch algorithm
I would like to ask why when we initialize 0 as the starting point, there are 3 gray boxes that are not used as shown (highlighted in the red box) in the pic?
Are these boxes to show that they are ...
5
votes
1answer
97 views
How to output all sequences with bwa mem, not `*`?
I've been running bwa mem -a for alignment, using the -a flag---this will
output all alignments for SE or unpaired PE
I've ...
6
votes
4answers
696 views
What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line
I have two DNA strings:
GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC
and
AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG
I want a tool that allows me to do something like this on the ...
3
votes
3answers
119 views
Fast and reliable alternatives to blast
After some unexpected results (and previously reported) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate.
I only found hmmer, but I don'...
5
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1answer
73 views
Does the “.full.aln” file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?
I have a number of sequences and a reference genome. I used snippy to align each individual sequence with the reference genome. I then used ...
5
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1answer
156 views
full visualisation of draft genomes alignment
I have two draft genomes (aprox. 500Mb each), one with ~10'000 scaffolds (genome1.fasta) and one with ~1'000 contigs (...
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1answer
32 views
Exporting nt's differences from MEGA alignment
I have an alignment of some full genome sequences of DENV1 that we have recently sequenced from the serum of patients. I have already cleaned the sequences, built the alignments and done the SNPs ...
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0answers
38 views
scoring matrices computation from transition probability matrix
The transition probability matrix over time t is computed as P(t) = e ^Qt. In order to calculate a general set of transition probability matrices what type of t values can be used ( t = expected ...
3
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0answers
82 views
Sequence alignment using BWT
My Problem:
Skipping some specific background, what I want to do is judging whether some soft-clipping sequences are the same, which may result by the same SV event. Colored bases in Fig.1 is an ...
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0answers
57 views
How to create a dendrogram of clusters and reconstruct phylogenetic relationship
I'm working with a Daphnia data set looking at the 16s gene pulled from the BOLD database. So far I did a multiple sequence alignment and attempted to cluster and plot a dendrogram:
...
4
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1answer
185 views
What are “split reads” and “intron clusters?”
I'm working through the example data set for LeafCutter and the documentation mentions "split reads":
This will cluster together the introns fond [sic] in the junc files listed
in test_juncfiles....
3
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0answers
46 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: ...
2
votes
1answer
81 views
Aligning sequence and comparing it against primer
I am looking to show how a primer is consistent among some genomic data. I have a primer of about 23bp and looking to compare it to about 5000 genomic sequences of 10kb. I am unsure how to format it ...
0
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1answer
81 views
Find a map/correspondence between two versions of a genome
I am working with two versions of the C. elegans genome. I am finding interesting regions (specifically, tRNA genes) in version 1 and then I would like to know if version 2 also has a tRNA gene in ...
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0answers
103 views
How to make year scale bar unit in figtree software?
I have generated phylogenetic trees for virus sequences by using beast software.
I observed in various research articles that the phylogentic trees also have a scale-bar (which mostly represents ...
2
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0answers
25 views
Alignment using secondary and tertiary features of DNA
I m trying to align different sequences of length not greater than 50. Is there any way to incorporate other information such as stacking energy, entropy, bonds etc. If there any way to align ...
4
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0answers
78 views
Merging ssu-align alignments
ssu-align is an HMM-based MSA tool for ribosome's small subunit (SSU) sequences. It's bundled with three SSU models: archaeal, bacterial and eukaryotic. Given a set of archaeal and bacterial sequences ...
8
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1answer
402 views
Better aligner than bowtie2?
Bowtie2 is probably the most widely used aligner because of it's speed. Burrow-wheeler (BW) algorithms (including bwa) tend to ...
2
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1answer
83 views
Interpreting bayesian phylogenetic model using Tracer?
I am doing phylodynamic analysis of virus sequences using bayesian method using BEAUti and BEAST. As a part of my analysis I am using Tracer to check how my model is working.
I can interpret some of ...
6
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1answer
61 views
Why aren't clustal alignments stable under deletion of some of the sequences?
I'm new to pairwise and multiple sequence alignment in general, but I thought I understood how clustal works -- k-tuple distance is a cheap metric that's 'probably approximately' monotonic in the real ...
8
votes
2answers
209 views
Is there a standard definition for “assembly polishing”?
Is there a standard definition for "assembly polishing" in the field?
Is there a standard definition for what polishing algorithms do?
My understanding of "polishing" is strongly influenced by ...
6
votes
1answer
354 views
BLAST(n): No hits found
I am currently exploring the BLAST program, just for testing purpose i generated two FASTA files, containing two genes A and B, such that B is just a motif of repeated 'G's that occurs in A.
file A....
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0answers
54 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:
...
5
votes
1answer
80 views
Are there certain alignment methods/tools which perform better with a high density of indels?
I have a set of experiments which should result in WGS reads with a high density of indels.
Question: Are there certain alignment tools/methods which perform respectively "better" with these reads? ...
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0answers
78 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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votes
1answer
128 views
Command not found error on HISAT2
I have been attempting to map reads to a reference genome using HISAT2 using the Pertea, et al 2016 Nature Protocols paper. I am able to successfully generate an index (using the hisat2-build command),...
5
votes
1answer
115 views
Evaluate clusters of individuals by using their sequence data
For a dataset of several hundred individuals, I applied a hierarchical clustering to generate clusters based on a functional trait that sets them apart.
My task is now to evaluate if these clusters ...
1
vote
1answer
89 views
Creating frequency plot from weblogo with frequency unit on the Y axis
Hello I am trying to create frequency plot for a motif with frequency unit on the Y axis from 0 -100 nt as the unit as represented in this paper.(Seiler et al., 2018)
6
votes
1answer
80 views
Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?
I believe that the human genome reference took DNA samples from different people and that some natural variation is included in extra contigs.
However, the human reference genome comes from a ...
5
votes
3answers
218 views
Generating the reconstructed alignment from BAM
I have a (small) BAM file with CIGAR and MD fields.
Question 1: What tools exists in Python and/or R to reconstruct the alignment between the reference and the read in a BAM? Given that this is a ...
2
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1answer
131 views
Can I export the SNPs between whole genome alignments using the command line?
I am using Mauve to align two whole genomes. I use the following command to get the alignment in xmfa format:
...
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1answer
91 views
Why is my STAR reference genome indexing aborting on my GNU/Linux server but not on my Mac OS X laptop?
I am running the following command to index my genome:
...
