Questions tagged [sequence-analysis]

Analysis of DNA, RNA or protein (amino acid) sequences. Here sequences are compared so analyze similarities and conserved regions. Sequence analysis is usually done by specialized software.

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Through which mechanisms did the Drosophila Histone Cluster evolve?

The Drosophila Histone Cluster is a gene cluster that contains more than a hundred copies of a sequence that encodes several histone proteins. These copies are very similar. My question is what ...
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Whole genome sequence analysis software

Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, ...
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Standard datasets for testing new multiple sequence alignment algorithms?

Are there any open and freely distributed standard datasets for testing new algorithms for multiple sequence alignment?
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How can sequence analysis establish whether a genomic sequence is a functional gene or a pseudogene?

BLASTX of a query gene shows 5 hits in my subject, how can I find out which of these are expressed and which are pseudogenes (using DNA sequence or by sequence analysis)??
Sinha S.'s user avatar
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Hiding identical sequences in NCBI web interface

Sometimes there are identical sequences in Genbank/Genpept, most often coming from the same species but different strains. Ie if I look up "bacteria chitin synthase", the 624-aa protein from Dickeya ...
Synedraacus's user avatar
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MSA cluster and MSA depth

I was reading the AlphaFold paper and had difficulty with a couple of terms introduced in the main text of the paper. I asked ChatGPT what these were but I'm not sure that it's accurate. I had a hard ...
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Zayed et al. (2022) "Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome"; expressed sequences or transcribed?

Phys.org's Ocean water samples yield treasure trove of RNA virus data summarizes Zayed et al. (April 7, 2022) in Science Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA ...
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It's right to say coding sequence is part of exon sequence?

Some basic ambiguities making me confused. I downloaded 5'UTR, CDS, 3'UTR, and exon sequences, separately from Biomart for a gene P4HA2 (Homo sapiens) and found some simple sequence repeat (SSR) on ...
Mary's user avatar
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Determination of gene direction

I have one sequence that composed of sequences of three genes. I should determine the direction of each gene, but two of these genes are disrupted, and I can't determine the initial codon. Does anyone ...
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Are there any examples of weighted edit distance genome alignments?

It has been said that weighted edit distance is a preferred way to compare/align genomes in practice, e.g., when identifying genetically similar patients. I wonder if there are some concrete examples ...
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How does one apply Bayesian inference to quantify a read the deeper you sequence?

For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule. What is the ...
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Genotype-Phenotype databases?

Beyond the Stanford HIV database, what other databases out there provide a dataset linking virus/bacterial genotype to quantitative phenotype? I'm looking for high quality datasets to test machine ...
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What are constrained genetic elements?

I am somewhat of a newbie in evolutionary biology currently taking my first steps in bioinformatics. I was reading a paper when I came across the term "constrained genetic elements", referring to ...
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Efficient algorithm to calculate various population divergence statistics

Intro and description of the data I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format ...
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Why are some protein sequences known but their 3D structure isn't?

Why are there some proteins that have a known amino acid sequence, but their 3D structure is not known? Wouldn't finding the former in a lab lead to the discovery of the latter? Please correct me if I ...
3michelin's user avatar
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What results would come from DNA analysis of several different types of DNA mixed together?

By "types," I mean several different species of animals. If, post extraction, the pure, isolated DNA of several different animals were mixed together and run through DNA analysis, I know the ...
FeywildWest's user avatar
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What is the difference between 4th generation sequencing and NGS?

The generation of sequencing technologies has come on leaps and bounds and there are stark differences between the types of technology used. There is a great Q&A here What is the difference ...
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What is the significance of cysteine in a protein sequence?

What is the importance of cysteine-cysteine in amino acid sequence? What can I infer if I get a high percentage of C from a protein sequence?
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Lysozyme amino acid sequence: N-terminal extension

I looked up the amino acid sequence of lysozyme here: http://www.biology-pages.info/L/Lysozyme.html Then I crossed referenced that with the lysozyme sequence on UniProt: https://www.uniprot.org/...
edmund shelto's user avatar
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What is the sequence similarity between humans and chimps in the noncoding genome?

I've seen some papers discuss extensively how human and chimp genomes compare in many of their features, eg Suntsova & Buzdin 2020, but I have not been able to find a paper that specifically ...
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Hierarchial and shotgun sequencing vs Massively Parallel Sequencing

Why is the cloning step unnecessary prior to sequencing with massively parallel sequencing (MPS; Illumina or similar technologies), when it is necessary for hierarchical and shotgun sequencing? I know ...
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Distribution of Exon and Intron Sizes

Goal I am trying to get a distribution of Exons and intron sizes in Three-Spined Stickleback (Gasterosteus aculeatus). Data downloaded I downloaded some data from Ensembl. More precisely, I went ...
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Where can I find DNA Sequence data for colon cancer

I am a computer scientist studying pattern recognition, and I am hoping to do some supervised learning on colon cancer. Unfortunately, I'm having a heck of a time finding DNA data in the following ...
Jonathan Charlton's user avatar
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Query from a ppt slide

I came across this slide: Now I haven't understood what the last two grey colored lines mean. Can't ORFS be of any size? What is overlapping frames here?
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what does sequences overlap indicate

what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other and how does one go on to ...
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Is it rare for a virus to be similar to its host?

Halomonas bacteriophage vB_HmeY_H4907 discovered recently in the Mariana trench is apparently highly homologous to its host: To our best knowledge, it is the deepest isolated siphovirus from the ...
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What is the typical arrangement of amplified genes in archaea genome?

I have to check if some genes are amplified with bioinformatics tools, but, in order to do it, I need to know what this means from a biological point of view. It seems not so difficult to understand, ...
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How to find the enhancer region of a specific gene?

I am new to these concepts in biology and need some help understanding. My main concern is how to find the enhancer of my gene of interest, specifically the sequence of the enhancer. I am working on a ...
Leon Camarillo's user avatar
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What tool can I use to align multiple protein sequences to one reference sequence?

I have a protein of interest which is ~300 amino acids in length. I also have around 40 short sequences (all 9 amino acids in length); these are all very different from each other. I would like to ...
agatha's user avatar
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Is there a system biology approach to compare pathways or famillies of proteins from an evolutionary point of view for the same organism?

I would be interested to know if there is a method/analysis or a set of methods to compare two groups of pathways or families of proteins. I would specifically be interested by a system biology ...
Dr. H. Lecter's user avatar
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How to interpret Percent identity matrix created by Clustal Omega?

I did a multiple sequence alignment using Clustal omega. checked similarity for 3 protein sequences : aspartyl aminopeptidase [Homo sapiens], aminopeptidase P (APP) [Plasmodium falciparum 3D7], yeast ...
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How is the GenBank used in typical biological research? [closed]

How is the GenBank used in typical biological research? According to the GenBank statistics, the database contains about 100 million sequences. I find it difficult to understand why is all that data ...
guest's user avatar
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Datasets of aligned nucleotide sequences [closed]

Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there? (I would like to use such datasets for training the alignment ...
Anas Elghafari's user avatar
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Can PolyA tails be within Expressed Sequence Tags?

Can polyA tails occur within (rather than at the end) of a sequenced tag? Consider, for example the following two sequences from NCBI: DY008075 ...
highBandWidth's user avatar
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Calculating sequence divergence score for a protein from identity or similarity score?

I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue ...
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Why use RRBS (reduced representation bisulfite sequencing) instead of general BiSeq?

My understanding is that RRBS is used for certain cases. For example, WGBS (whole genome bisulfite sequencing) is limited by repeated sequences. However, many papers seem to use both techniques. ...
ShanZhengYang's user avatar
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2 answers
166 views

Are there any major noticeable limitations to genome sequence compression methods that use reference templates?

Recently, I have been researching about big data analytics in biochemistry, and started wondering about how genome sequence compression could affect analysis. Of all the method listed on the ...
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What is the sequence of pPROLar.A plasmid?

I've been looking for the sequence of pPROLar.A122 plasmid but I haven't found it. Where could I find the sequence? The first link (addgene) on googling reports a plasmid which is reported to have ...
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Design arbitrary degenerate primers (with non-binding criteria)

I would like to design a number of arbitrary degenerate primers (primers with variable bases, e.g. NGATWGCTSATNGC) for a TAIL-PCR. I would like to be able to ...
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How do I find the sequence of the phage BxB1 gene?

Specifically, I'm trying to find the sequence of BxB1 and its att sites. I have success finding the att site sequences, but I'm having a bit more of an issue with finding the sequence of the actual ...
The Obscure Question's user avatar
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how to reconcile PDB structures' sequences via Uniprot references?

I’m trying to reconcile structures in PDB entries with their sequences as reported in their chemList.polymer.dbref entries. E.g.: considering structures for HIV ...
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Applying Constraint Programming to sequence alignment/analysis

My Masters program is focused on formal methods such as SAT solving and constraint programming. I am interested in applying such techniques to problems in sequence alignment and sequence analysis, ...
Anas Elghafari's user avatar
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1 answer
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What is the close and related genome used for in Gene models?

all I am a little bit confused about using the related genome or reference genome. When we have a reference genome, we can do alignment. Also we can do the assembly. Can you give some more reason ...
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Quantifying Hydrophobicity from amino acid sequence

fourth-year undergrad here so any help is super appreciated! Also this is not something I am working on for a grade, so pls don't think I am just looking for someone to do my homework lol! In a gist, ...
Hannah Lye's user avatar
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How to interpret different results from Clustal Omega and Multalin?

I have been working on aptamers, which are nucleotide sequences. They bind to various targets, in my case a particular cell surface receptor. The people associated with the project performed SELEX and ...
Abhishek Bastiray's user avatar
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How to know which residues belong to the variable or constant regions of a Fab (fragment antibody)?

I have a fragment of antibody (Fab) structure, and I know its amino acid sequences of its heavy chain and light chain. As each chain of Fab can be divided into variable and constant regions, how can I ...
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How to calculate RPM?

I´m just starting my postdoctoral fellow and my new project involve sRNA Deep Seq. I´m having problems with the data normalization. I´ve been reading papers about it and the variety of normalization ...
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What are the exact reason causing missing calls in a VCF file from exome sequencing?

My data is a VCF file from exome sequencing variant call. I'm not very familiar with the sequencing process and variant calling process. I noticed that there are some missing genotypes, which is ...
Yan's user avatar
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Where are examples of Interspersed repeats? [closed]

Interspersed repeats are often defined as repetitive sequences dispersed throughout the genome. However such definition (IMO) does not exclude Tandem Repeat Sequences. So I started to search for ...
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Why do we use klenow fragment in pyrosequencing?

Why do we use klenow fragment in pyrosequencing instead of polymerase
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