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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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?

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 regular Tries in the following way: If there ...
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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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 ...
RPINerd's user avatar
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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
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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
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Seeking Guidance on Designing DNA Sequences with Specific Criteria

Dear Bioinformatics Community, I hope you're all doing well. I am currently working on a project that requires designing a DNA strand or more, every 10 nucleotides long (preferably), with specific ...
Hashem's user avatar
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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 ...
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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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1 answer
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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
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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
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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
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1 answer
74 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
115 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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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?
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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 ...
Yano's user avatar
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Why does the Smith-Waterman algorithm have a complexity of $O(m^2 \times n)$?

I recently read that original the Smith-Waterman algorithm to do a local pairwise alignment of sequences has a complexity of $O(m^2 \times n)$, where $m$ and $n$ would be the lengths of the sequences ...
Gordon J. Köhn's user avatar
3 votes
2 answers
189 views

What can be the bias of aligning paired-reads in a single-end mode?

I don't know if I'm in the right place but I have a technical problem to fix. I would have to align paired-end reads from Illumina sequencing to compare a normal genome with a tumor one. When I align ...
cucalorda's user avatar
3 votes
0 answers
446 views

Aligning PacBio HiFi reads to reference genome using pbmm2

I am trying to align a yeast strain sequenced by PacBio HiFi reads to the reference genome S288C (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/) using pbmm2 but for some reason I am ...
rimo's user avatar
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2 votes
1 answer
284 views

How to calculate average BLOSUM62 scores?

I can understand the motive behind the BLOSUM62 matrix, this being a pairwise mutation matrix describing aggregate mutations between the 20 amino acids. However how would you calculate the average ...
dallas_engineer's user avatar
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Relationship between molecular weight and linear peptide

Sorry for this very beginner homework question: Which of the following linear peptides is consistent with Spectrum = {0 71 99 101 103 128 129 199 200 204 227 230 231 298 303 328 330 332 333}? (Select ...
kevin's user avatar
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1 vote
1 answer
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How to chop fasta / bed /peak file genomic segments into smaller fixed or custom genomic intervals

I am trying to split my .bed/.fa file genomic segments into arbitrary smaller overlapping intervals: Consider a typical line/row in my *.bed file as follows: chrom. $\ \ \ \ \ $ start $\ \ \ \ \ \ \ \...
Zebra Fish's user avatar
2 votes
1 answer
63 views

What is the best way to process yeast genomes?

I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis. I have a reference genome (S288C) to use for ...
rimo's user avatar
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1 vote
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The difference between sequence-independent and sequence-order independent structural alignment?

I am confused about the difference between sequence-independent and sequence-order independent structural alignment. TM-align for example claims to be sequence-independent; however, I've seen it is ...
fcan's user avatar
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2 votes
2 answers
1k views

How to convert fasta alignment to nexus or phylip format?

I generated a multiple sequence alignment using mafft, but I would like to convert it to nexus or phylip format (required by a downstream software). What's the easiest way to do the conversion?
Kamil S Jaron's user avatar
2 votes
1 answer
569 views

PyMol alignment script

Is there a way write a script in python to use "super" to align proteins from a 2D array? Each row of the array has 2 columns, and for each row, I want to "super" the two proteins (...
Jennifer S.'s user avatar
1 vote
1 answer
73 views

Lower case vs. upper case nucleotids in sequence vs. dots at the end

What is the difference between lower case and upper case nucleotides in a sequence? My other question is what are the dots at the end of the sequence? Some examples are shown below: GGgG,GGgG,GGgG,...
David Khutsishvili's user avatar
3 votes
0 answers
37 views

How are BLAST record scores calculated in biopython

Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
Tim Kirkwood's user avatar
3 votes
2 answers
158 views

How can I find the maximum percent identity between two sets of (unaligned) sequences?

As the title states, I've got two sets of unaligned amino acid sequences (~25k sequences in one, ~3k in the other). I want to find the minimum distance between a sequence in the first set and a ...
Empiromancer's user avatar
3 votes
2 answers
2k views

STAR vs Bowtie2

What is the fundamental difference between STAR and Bowtie(2). Specifically, what is the difference in their final output (regardless of run-time differences, speed, memory usage etc.). Both seem to ...
Zebra Fish's user avatar
1 vote
0 answers
233 views

Most reads no_feature with htseq-count

I have mapped reads to the yeast (R64-1-1) genome with STAR like this: ...
justinian482's user avatar
1 vote
1 answer
34 views

Multifasta protein alignment

I have around 4000 orthologous proteins for each of 5 species, I'd like to align them and to concatenate alignments. Which tools can I use? And how? Marco
Marco's user avatar
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2 votes
1 answer
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Statistical significance of pairwise protein sequence alignment

I have identified a conserved region in a protein I'm studying, by doing multiple sequence alignments against a dozen of its orthologs. I've then found that this region also aligns relatively well ...
gaspanic's user avatar
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1 vote
1 answer
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Aligning scRNA-seq fastq to .bam without cell barcodes

I would like to convert the fastq files from this dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98679 to .bam files. The group did not provide the scripts they used to to their ...
Angus Campbell's user avatar
1 vote
1 answer
39 views

Problem with sequence alignment

I'm trying to find if the peptides in column A are present within the longer peptides of column B. Pairwise alignment tools take the data from both columns as one string (i.e., TIIDYTNNHYTNNHLEII... ...
Parasu Nagesh Sunag's user avatar

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