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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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What is the Impact of Adjusting the -reward Parameter in KMA Aligner?

I am currently utilizing the KMA aligner developed by Clausen et al., as detailed in their BMC Bioinformatics article (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6). ...
dim's user avatar
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Understanding the Relationship Between ConClave Score, Depth, and Template Length in KMA Aligner Results

I am currently analyzing my nanopore metagenomic sequencing data. After demultiplexing and trimming, I am using the KMA (k-mer alignment) aligner by Clausen et al. (https://bmcbioinformatics....
dim's user avatar
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How can I include the start and end sequence number while doing MSA alignment with any alignment tool like CLUSTALW?

I have this assignment to align sequences from the domains of 5 different proteins. I extracted the domain sequences. I have done the alignment, but I realize I need to number each sequence (since ...
Ruthy's user avatar
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2 answers
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How to align two FASTAs and extract the aligned part?

I have two fastas and I'd like to align them to extract the aligned part. I've just found examples (Several of them) of alignment of FASTQs using FASTA references, so I'm not sure if what I want ...
dyxcvi's user avatar
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5 votes
1 answer
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Waterman-Smith-Beyer implementation in Python

I am working on a text aligner to help me get a better understanding of specific steps necessary to perform sequence alignment. So far, things have been going great but I noticed yesterday that my ...
dawnandrew100's user avatar
1 vote
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Guidance Required on Prioritizing Columns for Gene Expression Analysis Using KMA Tool

I am currently in the process of comparing two distinct sets of genes that have been sequenced under two different conditions. My objective is to ascertain whether the expression of specific genes in ...
dim's user avatar
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Problems with pbmm2 alignment after subsampling

I have tested pbmm2 align on my total set of reads. However, the alignments are poor. Therefore I am trying to optimize the parameters with a few of them. After doing a subsampling with samtools -s 0,...
María José's user avatar
3 votes
1 answer
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Passing data from the Agilent Trimmer utility to bwa-mem2 via a named pipe

I am trying to use a named pipe to pass data from the Trimmer utility from the AGeNT toolbox from Agilent, through bwa-mem2. The normal behavior is that the Trimmer utility writes trimmed fastq files ...
Harry Matthews's user avatar
1 vote
1 answer
18 views

Where to obtain fastq_illumina_filter

I'm setting up a snakemake pipeline for my lab, and I'd like to install fastq_illumina_filter. All links I can find point to this address for info on it, but the website seems to be down. Is there ...
Whitehot's user avatar
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Creating a Multiple Sequence Alignment From Eggnog Mapper Results

I used Eggnog mapper to annotate several rockfish genomes and the output files have qstart and qend values for each gene. I plan to use the phylogenetic trees for a few different genes for positive ...
Aidan Larish's user avatar
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Large skip after aligning using Cellranger

I have a read from BAM file as following ...
Tien's user avatar
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1 answer
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How can I Find DNA sequence of promoter region of a gene?

I have a fungal sequence from Candida albicans, sequenced via Sanger sequencing, that I want to check for quality and contamination. I have 2 questions: Could I use Alignment ? or BLAST or ...
atp's user avatar
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1 vote
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How to compare CDS, CNE, miRNA, UCNE across new related genomes?

I have 5 sets of raw Illumina whole genome shotgun data from 5 different species, and 3 reference genomes that are assembled/annotated, I want to produce a similar table to Table S2 of this paper: ...
JohnDoe23's user avatar
2 votes
1 answer
63 views

Aligning FASTQs to FASTA reference

I'd like to align some FASTQs to an average mtDNA FASTA file that I have downloaded so I can have the human mtDNA isolated from those FASTQs. For that, I used bowtie2. Can I expect that after running ...
dyxcvi's user avatar
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How to create a dataset of contact maps of homologous proteins?

Disclaimer: I am a machine learning researcher working on network science and want to use proteins to test an algorithm of mine using real-world data. My bioinformatics knowledge is minimal. I need to ...
Tendero's user avatar
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How to download the same 18S rRNA gene region for multiple species?

I need 18S rRNA gene sequences for a wide variety of eukaryotic species. I know that Ensembl has this gene sequence, but I don't understand what is the correct protocol to download the sequences. I ...
Mirk's user avatar
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1 answer
102 views

All against all sequence alignment

I have a large set of protein sequences and would like to create a "similarity matrix" out of them (for phylo trees later). So I have to run n(n-1) ...
El Dude's user avatar
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1 vote
2 answers
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How to know if FASTQ/BAM is from reference genome (FASTA)?

I'm new to bioinformatics. I have a problem in which I have a FASTA reference genome and lots of reads in FASTQ files. Some of them could be contaminants, so I'd like to filter them out and get only ...
dyxcvi's user avatar
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2 votes
1 answer
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Salmon Multiple File SCRIPT giving error

Hi I am using Salmon quantitation for multiple fastq paired files using following code ...
S_Malik's user avatar
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4 votes
1 answer
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split fastq file containing a sequence block at different locations

I have some fastq files (obtained from nanopore sequencing) that contain reads that can be of either of these 5 forms: a known CDS with 3'UTR: ...
jetpacks_reno's user avatar
4 votes
1 answer
55 views

Finding homologous regions in multiple whole genomes

Right now I have six genomes that I want to compare and identify homologous regions in the genomes. I have run nucmer, show-coords and obtained the output files. An example is shown below with Genome ...
LORL's user avatar
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6 votes
1 answer
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How many false positive duplicates are marked using just the position of first unclipped base?

In the popular picard MarkDuplicates tool, a read is marked as a duplicate if it has the same position as another read starting from their first unclipped base in ...
Ricky's user avatar
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3 votes
2 answers
82 views

What is the best way to acquire protein isoform sequence alignment?

[Update] Thanks @terdon. To clarify my question: I have a bunch of protein isoforms sequences (produced by the transcripts in the figure) and I want to align protein products (e.g., proteins produced ...
Jen Marylin's user avatar
4 votes
2 answers
82 views

probability of finding a 5 amino acids in a row within a proteome

How to calculate the probability of finding two proteins that share a 5 amino acid long motif from a proteome of around 1067 proteins that have an average length of 65 residues. The probability of a ...
saplingmagic's user avatar
1 vote
0 answers
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java.lang.ArrayIndexOutOfBoundsException: Index 86 out of bounds for length 86

I use the next versions: gatk 4.4.0.0 minimap2 2.26-r1175 samtools 1.19 I have a fastq file. And try to implement gatk MergeBamAlignment to generate a new ...
Shwarz's user avatar
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2 votes
1 answer
99 views

align to the whole hg38 genome, then split bam and collect metrics on each bam issue

I am doing some coverage analysis on deep sequencing human genome. I first align to the whole hg38 genome, then split bam to each chrom, and collect metrics on bam for each chom. I first split using ...
cautree's user avatar
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5 votes
2 answers
215 views

Why are Minimap2 alignments different with CIGAR generation flag?

I am using Minimap2 (v2.26-r1175) in Linux to generate a sequence alignment between the Streptomyces coelicolor A3(2) chromosome (ref.fa) and the Mycobacterium ...
Gawain's user avatar
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2 votes
0 answers
173 views

Fst calculation from VCF files

I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
hina's user avatar
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0 votes
1 answer
114 views

Aligning sequences with multiple genetic codes!

I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic codes. I work with fasta files that contain sequences of protein coding ...
George X.'s user avatar
4 votes
2 answers
183 views

BioPython bootstrap is not reliable?

Here i will show you a minimal working example of code and as you can see the support values for the tree is always 100. I am using synthetic sequences of 100bp for 6 elements. The sequences have been ...
Mirko's user avatar
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1 vote
0 answers
149 views

bwa mem hangs after a few thousand reads

I am trying to align a bunch of paired sample fastq files using bwa mem. My original command was: ...
padakpatek's user avatar
1 vote
1 answer
43 views

What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?

This question was also asked on reddit Tries are a data structure that can be used to efficiently store and search for strings. Tries created from an ordered sequence of strings differ from the ...
GEP's user avatar
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0 answers
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Estimating rate of evolution from a phylogeny

Any suggestions for the best way to estimate a metric for evolutionary rate of viral sequences of the same species? I was using terminal branch length from a phylogeny and would quite like to try sub ...
Nitara Wijayatilake's user avatar
3 votes
2 answers
77 views

Sequence Alignment for sequences with the same length

I am doing research on a new method of optimizing sequence alignment process (Needleman - Wunsch algorithm) but the idea would only work with sequences that have the same length. I am wondering if ...
MirzaK's user avatar
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0 answers
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Problem with edit and align viral whole genomes

I have a database of whole genome of African swine fever virus (about 190kb/genome) downloaded from GenBank. But these sequences do not start at the same place on the genome. When I align the sequence ...
tiep tran's user avatar
4 votes
2 answers
184 views

How to create a phylogenetic tree from diverse mitochondrial genomes

I would like to create a phylogenetic tree for the most species in my dataset. I'm starting with around 1200 species, but since it's not good practice to align short and long sequences I tried ...
Mirko's user avatar
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3 votes
2 answers
122 views

Cannot obtain alignment summary after running Bowtie2

I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following: ...
ALEJANDRA PANDO CACIANO's user avatar
2 votes
1 answer
40 views

Find protein in DNA sequences with arbitrary encoding and possible frameshifts

I have a dataset with lots of DNA sequences (~10 M seqs, each ~6 KBp long). I want to detect presence of a fixed given protein (~600 Bp / 200 aa) within each sequence and, if detected, obtain the ...
cos_theta's user avatar
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2 votes
1 answer
36 views

What does the different sequences represent?

I am using this package nsdpy to download genome sequences from NCBI nucleotide database. Specifically I am interested in the whole mitochondrial genome of different species, here I will use a subset ...
Mirko's user avatar
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1 vote
0 answers
60 views

SNP How to detect regions of erratic pairwise alignment?

I have clusters of DNA sequences that contain some mutations. All the sequences in a cluster should contain the same mutations. As the mutations aren't known, those clusters of sequences were pairwise-...
Fravadona's user avatar
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0 votes
1 answer
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Mapping List of Probes/Primers/Short Oligos to a Reference Fasta/q

Could you help me bioinformatics SE people. So I have been duckduckgo-ing up a storm and even consulted the AI overlords and haven't come up with a solid way to do this, but it is so fundamental to ...
RPINerd's user avatar
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0 votes
0 answers
37 views

Error while opening xmfa generated by progressiveMauve

I used commandline progressiveMauve to align two genome .gbk files. The alignment was successful. But when I try to visualize the final .xmfa file with Mauve, I get the following error. ...
venkatesh war's user avatar
1 vote
1 answer
59 views

Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average

I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine... except some of the codon ...
Sudoh's user avatar
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1 vote
0 answers
185 views

Pacbio HIFI pbmm2 alignment metrics

I am new to pacbio sequencing data. I just did some alignment of pacbio HiFI data using pbmm2. I have the bam now, I would like to collect some metrics on the alignment. I used to work on the illumina ...
cautree's user avatar
  • 139
1 vote
1 answer
338 views

How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?

When we run the OrthoFinder analysis tool on a group of genomes to get the orthologues shared by them one of the output files include a folder named 'Species_Tree' that contains a text file named '...
K_081's user avatar
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1 vote
0 answers
199 views

Mapping statistics from the bam files

I would like to find the mapping statistics from the sorted bam files. Samtools flagstat gives the output only for a single file. What is the easiest way to find the mapping statistics for all ...
Kam's user avatar
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2 votes
2 answers
60 views

RNAseq alignment: best practices for aligning to multiple isoforms?

I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions. Many of my (de novo assembled and ...
DavidR's user avatar
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0 votes
1 answer
112 views

Is my reference sequence too small?

I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I ...
rimo's user avatar
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3 votes
0 answers
26 views

Add or Simulate Noise in Short-Read Paired End Data

For a project I'm working on, I need to figure out how to model noise that may be happening in real genomes due to alignment errors, contamination, etc. Specifically, short-read paired-end data either ...
user avatar
3 votes
1 answer
95 views

Sanger Sequencing Knitting Error

I am doing a project where I am reproducing the analysis from the article "sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R". Below is the example chunk for ...
Taeen Jidaan's user avatar

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