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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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89 views

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 ...
1 vote
1 answer
76 views

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, ...
3 votes
2 answers
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Why UniRef representative sequences in UniProt are so long?

I found that some sequences in UniRef90 database are tens of thousands amino acids long. I read UniProt official documentation and figured out that these sequences are the representative sequences of ...
2 votes
1 answer
296 views

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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1 answer
244 views

Sequence identity and coverage in multiple sequence alignment of proteins

This might be naive since I am very new to the field, but I wonder about the difference between sequence identity and coverage in multiple sequence alignment of proteins. I imagine the calculation ...
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1 answer
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How to convert enrichment/depletion to frequency for comparing deep sequencing to sequence profile?

I have two datasets, from different sources, that I need to compare. The first set is deep sequencing results of a directed evolution experiment, where I have the naive library and selected library ...
1 vote
1 answer
76 views

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 ...
5 votes
3 answers
736 views

What is the state-of-the-art algorithm for multiple sequence alignment?

Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment? How big is the need for better algorithms? How many sequences need to be alignment in a ...
8 votes
3 answers
9k views

What is the difference between sequence alignment and sequence assembly?

I read the wikipedia page about sequence alignment and sequence assembly but I have not been able to find any difference between the two. What is the difference between sequence alignment and sequence ...
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2 answers
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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 ...
1 vote
1 answer
109 views

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 ...
7 votes
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How are DNA virus cladograms actually calculated in practice? Is the procedure different for RNA viruses? Are these processes somewhat subjective?

The May 24, 2022 Bloomberg opinion piece Monkeypox Isn’t Looking Like a Covid-Sized Threat; It’s still early, but contact-tracing efforts and analysis of the virus’s genome offer hope that this ...
1 vote
1 answer
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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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1 answer
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Alignment given two sequence

I have two sequences and I need to perform sequence alignment to determine all possible sequence alignments. I have created the matrix and managed to find 16 alignments. I wanted to understand if I ...
2 votes
1 answer
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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 ...
4 votes
1 answer
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Is it possible to establish a newer animal model completely based on Bioinformatics studies?

I wanted to know, if it is possible to prove a new organism as an animal model for any human disease by only Bioinformatics methods like NGS and Structural bioinformatics. For Example, let's say ...
1 vote
1 answer
954 views

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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Is there a newer/better book than Genome-Scale Algorithm Design available? It's from 2015

I'm considering buying the book "Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing" by Veli Mäkinnen and others. However, as this book was ...
5 votes
2 answers
912 views

Meaning of ‘motif’ in molecular biology

I would like to understand the meaning of the term motif as used in molecular biology. In an article in Nature Biotechnology, Patrik D’haeseleer states: Sequence motifs are short, recurring patterns ...
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2 answers
8k views

How to check if a fastq file has single or paired end reads

I am trying to check if a fastq file has single or paired end reads. How can I achieve this with an error-proof method? I checked wikipedia and MAQ but I want to know if is there a reliable document ...
1 vote
1 answer
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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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180 views

Extract mutations from fasta sequences

I have a large amount of protein sequences in the .fasta format and I would like to extract only the amino acid mutations from these sequences, so that, in the end, I want to have a list that looks ...
1 vote
1 answer
260 views

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 ...
0 votes
2 answers
1k views

How to calculate the occurrence of a stretch of nucleotides in a genome?

I have seen that the formula to calculate the number of times a given sequence of nucleotides occur in a target genome is derived from that to calculate the expected frequency of restriction sites: <...
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1 answer
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Looking for study/genome data for HIV in different organs

I am looking for a research study or data base that has HIV genome data available in fasta or similar format. Specifically I need genome data of HIV taken from different organs in the same subject. I ...
3 votes
1 answer
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Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in ...
1 vote
2 answers
632 views

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 ...
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2 answers
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Sequence of DNA

While giving an amateur reading to DNA. I was stuck within the first few lines: Refined resolution of the structure of DNA, based on X-ray crystallography of short synthetic pieces of DNA, has shown ...
1 vote
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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 ...
-1 votes
1 answer
223 views

Convert fasta to ascii?

Is there an algorithm or tool to convert a fasta sequence file (such as the file linked below) into an ascii file for the purpose of gene synthesis? https://www.rcsb.org/fasta/entry/6EQJ To the best ...
-1 votes
1 answer
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Available Protein sequence alignment dataset and HMM model

I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to generate noisy copies of the consensus sequence ...
1 vote
1 answer
291 views

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 ...
1 vote
3 answers
895 views

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 ...
2 votes
1 answer
1k views

What do lower case nucleotides mean in this gene sequence?

The following table (image linked below) shows promoter sequences recognized by different sigma factors. The sequence given for, e.g. sigma B is "GTTTaa"; why are the "a"s lowercase? (from "A sigma ...
0 votes
1 answer
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Why does deamination in the lagging strand lead to an increase in the relative number of guanine and thymine to cytosine and adenine?

My question arose from this article on Wikipedia on the GC-skew in bacterial genomes: https://en.wikipedia.org/wiki/GC_skew As far as I understood, the lagging strand (the template strand), during ...
7 votes
2 answers
863 views

Comparative evolutionary study: is amino acid or nucleotide comparison more useful?

I am a high school student and am currently learning about evolutionary relationship study in biology. My teacher said that a comparative study of amino acid sequences is more useful than a ...
1 vote
1 answer
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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 ...
1 vote
1 answer
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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/...
1 vote
0 answers
841 views

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 ...
9 votes
4 answers
2k views

If we sequenced the genome of every species, would all phylogenies agree?

The Tree of Life is still up for debate. Most of this debate seems to be due to a lack of genomic information, but that deficiency is decreasing rapidly with advances in technology and sequencing ...
12 votes
1 answer
456 views

Which is the reference 16S rRNA?

Recently, I've stumbled upon a fact, which hasn't bothered me for many years. The fact is that all universal 16S primers are written as "[FR][0-9]+" (in regex notation), that is they have a position ...
2 votes
2 answers
139 views

Methods for microbial identification in soil

I'm trying to perform a survey of the life in a soil sample. I want to know what species of bacteria, fungi, and other organisms are in it. I've heard that ITS sequencing and 16S rRNA sequencing are ...
0 votes
3 answers
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why and how multi allele gets reported during variant calling in vcf?

This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can ...
1 vote
1 answer
321 views

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 ...
8 votes
4 answers
8k views

Significance of upper-case, lower-case and Ns in UCSC DNA files

I have downloaded human chromosome's data from UCSC FTP. Some part is in small alphabets and some is in large alphabets. Does it show the coding and non-coding region? Here is an example from the ...
5 votes
2 answers
1k views

List of proteins by number of amino acids / chain length

Is there any protein database online where I could obtain a list of proteins ordered by the length of their chains / number of amino acids, starting from the shortest, as well as to see their amino ...
39 votes
3 answers
98k views

What is the difference between local and global sequence alignments?

There are a bunch of different alignment tools out there, and I don't want to get bogged down in the maths behind them as this not only between software but varies from software version to version. ...
1 vote
2 answers
2k views

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?
11 votes
1 answer
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Sequence evolution simulation tool

I'm looking for a tool to simulate sequence evolution given a specific mutation model and birth-death model. I'm aware of tools and packages like INDELible, Seq-Gen and PhyloSim, but they simulate ...
1 vote
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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 ...