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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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 ...
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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: ...
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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 ...
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Any other (good) long read aligners apart kma?

I wonder if there are any other more efficient long read aligners apart kma? I have heard there is some hisat2 long read application but it's not really efficient. Any suggestions?
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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 ...
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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 ...
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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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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 ...
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Salmon Multiple File SCRIPT giving error

Hi I am using Salmon quantitation for multiple fastq paired files using following code ...
Malik Saad's user avatar
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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
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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 ...
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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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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
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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
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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 ...
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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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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 ...
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Fst calculation from VCF files

I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
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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
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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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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
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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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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
2 votes
2 answers
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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 ...
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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
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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
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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
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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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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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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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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 ...
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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
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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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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
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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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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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Automated method to figure out whether a recognition site is conserved or not using the results of simulated restriction digestion

Restrict from EMBOSS Suit version 6.3.1 with the following parameters: snucleotide1, sitelen = 4, rformat = table, enzymes = enzymes.txt. From the 4379 enzymes present in REBASE, we selected the 650 ...
Freezing Soul's user avatar
2 votes
2 answers
55 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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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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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
91 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
1 vote
1 answer
101 views

Phylogeny building in R from FASTA files:

Im working on building a phylogeny from scratch with downloaded FASTA sequences from GeneBank. I think Im doing alright up until the multi sequence alignment in the ...
I Del Toro's user avatar
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1 answer
124 views

How do I build the MinusB database for Kraken2? (Taxonomy issues)

I am attempting to build my own custom database for Kraken2. I have two questions: If I have the MCPyV genome in a file called MCPyV.fasta, how do I build a database with just this? How do I build ...
InterestingQuestions61's user avatar
3 votes
2 answers
103 views

How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?

I encountered the dichotomy in the context of PDBx/mmcif files, say, 6OSQ: each chain has a _entity_poly.pdbx_seq_one_letter_code...
rtviii's user avatar
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3 answers
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Read Clustal file in Python

This question was also asked on StackOverflow I have a multiple sequence alignment (MSA) file derived from mafft in clustal format which I want to import into Python and save into a PDF file. I need ...
Denise Lavezzari's user avatar
1 vote
1 answer
85 views

Maximum likelihood estimation for tree construction

Could someone direct me to a resource (textbook chapter, lecture notes, online video, etc.) that demonstrates, in a mathematically or computationally rigorous way, how to use maximum likelihood ...
DataScienceNovice's user avatar
1 vote
1 answer
142 views

Matches, mismatches and indels

I have a bam-file of reads and reference genome. How can I located matches, mismatches and indels in three different files with Phred score in each data of the files?
Shwarz's user avatar
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3 votes
1 answer
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heatmap of specific sequence motifs in aligned fasta files

I have a collection of fasta files, each containing three aligned sequences. I am interested in understanding the distribution of a specific sequence motif PGP, RGP and KGP in all the alignments. I ...
Jalan's user avatar
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1 vote
2 answers
123 views

How can I align two novel sequences to a reference genome and build a phylogenetic tree?

I have two new amino acid gene sequences that I want to align to a reference genome. Is it a good idea to have a combined phylogenetic tree? what will this type phylogenetic analysis called?
Echo94's user avatar
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1 vote
1 answer
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How to identify sequence origin in DNA shuffle reads?

The data I have a large number of reads from sequences that were generated by randomly shuffling regions of two parent sequences together. See the following image: The regions that are shuffled are ...
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