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.
139 questions
2
votes
1
answer
34
views
Finding antibodies sequence online
Not sure if this is the right section to ask this question but here we go.
I want to find human GPCR antibody sequences online and download them. I had some trouble finding good platforms with good ...
0
votes
0
answers
194
views
What is a reference strain in DNA-DNA hybridization DNA groups?
Results
DNA groups identified:
All intra-group relatedness values are shown in
Table I.
By means of reference strains, most of the DNA groups could be identified as groups described by Bouvet & ...
3
votes
2
answers
239
views
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 ...
1
vote
1
answer
92
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 ...
2
votes
1
answer
633
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 ...
0
votes
1
answer
530
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 ...
3
votes
1
answer
325
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, ...
1
vote
1
answer
82
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 ...
1
vote
1
answer
142
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
2
answers
1k
views
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
108
views
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 ...
0
votes
1
answer
315
views
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
142
views
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 ...
1
vote
1
answer
1k
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 ...
0
votes
0
answers
31
views
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
1k
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 ...
1
vote
1
answer
90
views
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, ...
1
vote
1
answer
322
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
2k
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:
<...
0
votes
1
answer
24
views
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
53
views
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 ...
0
votes
2
answers
98
views
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
2
answers
780
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 ...
-1
votes
1
answer
262
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
126
views
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 ...
0
votes
0
answers
195
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
392
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
1k
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 ...
7
votes
2
answers
1k
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
47
views
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
163
views
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
877
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 ...
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 ...
2
votes
2
answers
155
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
1
answer
101
views
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 ...
0
votes
3
answers
253
views
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 ...
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 ...
1
vote
0
answers
81
views
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 ...
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 ...
0
votes
1
answer
279
views
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 ...
0
votes
1
answer
299
views
Breakpoint resolution for copy number variation analysis
I am reading [1].
One limitation of the Read Depth approach is that "the breakpoint resolution is often poor". Which is the meaning of low-resolution breakpoint in this case?
Breakpoint is ...
0
votes
1
answer
278
views
Confirming exon shuffling in a gene
I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, gene sequence, and mRNA (with defined exon/intro ...
1
vote
0
answers
224
views
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 ...
0
votes
1
answer
40
views
Is there a database for immunoglobulin domain structure?
is there a database where I can find the sequences of the hypervariable domain of immunoglobulins and the sequences of the related antigens? Thank you
1
vote
0
answers
42
views
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 ...
1
vote
0
answers
180
views
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 ...
3
votes
0
answers
167
views
Difference between Classic Satellite DNA and Microsatellites/Minisatellites
I am very new to this community and have a basic question about repetitive DNA sequences.
How is different (classic) satellite DNA from microsatellites/minisatellites?
All textbooks give concrete ...
3
votes
2
answers
67
views
An efficient and free method of assembling a large number of Sanger sequencing reads?
I have a rather large number of Sanger Sequencing reads.
Is there a automated method in either Ugene or a similiar freeware that allows you to quickly assemble forward and reverse reads. Ideally ...
2
votes
1
answer
625
views
Which DNA sequence will have higher melting temperature: CCCCCC... or GCGCGC...?
I tried this service to calculate temperatures. The nearest neighbour method consistently gives larger results for sequences like GCGCGC over sequences like ...
1
vote
0
answers
178
views
Why do we use klenow fragment in pyrosequencing?
Why do we use klenow fragment in pyrosequencing instead of polymerase