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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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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 ...
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1answer
308 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 ...
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2answers
59 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 ...
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3answers
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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 ...
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1answer
181 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 ...
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1answer
35 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 ...
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4answers
6k 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 ...
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2answers
112 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 ...
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3answers
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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. ...
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2answers
1k 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?
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1answer
697 views

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 ...
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11 views

Better algorithm than Burrow-Wheeler, for aligning short reads with high number of mismatches

Burrow-wheeler (BW) algorithm is probably the most widely used aligner out there. Largely it is popular because of it's speed and tendency to not take much memory. However, it has limitations when it ...
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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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Quantifying loss of mtDNA using genotyping arrays

I recently read that mitochondrial DNA (mtDNA) levels can be measured by relative real-time PCR. Would it also be possible to estimate the degree of loss of mtDNA from genotyping array data?
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1answer
175 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 ...
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1answer
132 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 ...
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1answer
190 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 defined ...
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0answers
124 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 ...
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1answer
29 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
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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 ...
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0answers
137 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 ...
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0answers
119 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 ...
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2answers
56 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 ...
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1answer
873 views

How to do multiple sequence alignment?

I have a DNA sequence that makes protein 1. but now I have asked to: compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi sequence alignment (MSA) of the ...
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1answer
584 views

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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1answer
700 views

Standard practice for generating rarefaction curves from Next Generation Sequencing data

We have a few million 18S reads from a particular environment. The reads have been clustered into Operational Taxonomic Unit (OTU), and the OTUs annotated against a reference database. To generate a ...
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1answer
123 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 ...
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133 views

Why do we use klenow fragment in pyrosequencing?

Why do we use klenow fragment in pyrosequencing instead of polymerase
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1answer
39 views

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)??
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1answer
6k views

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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1answer
43 views

Which analytical techniques could you use to research relationships between 2 proteins? [closed]

Two of the proteins I am researching are known to interact. However, I would like to know if they interact with other proteins as well, and possibly form a pathway. Which analytical technique(s) I ...
6
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1answer
135 views

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 ...
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0answers
53 views

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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1answer
6k views

What are Codominant vs Dominant Genetic Markers?

When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions. Foll and ...
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1answer
55 views

What factors should I consider when selecting a reference genome for mapping?

I am under the impression that the most recent reference genome is typically the best case. What other things should I consider when selecting a reference genome? For example, is there any particular ...
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1answer
43 views

Difference in variance of Cys in protein sequences [closed]

Suppose I have got two sets of proteins (amino acid sequences). In one set, I find that the variance in the percentage concentration of the Cys is way more (65.34) than the variance of Cys in the ...
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2answers
1k views

Creating a Phylogenetic tree using DNA sequences [closed]

I was wondering given DNA samples, how can we create a phylogenetic tree? I mean I don't even want to have actual DNA sequence. Can I generate small samples, like reads of a length 100 or 1000 of ...
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0answers
70 views

C to T Transition Mechanism

I am seeing C to T transitions in my sequencing data, but also some strange signatures that follow along with that. I am trying to understand the biology of what is occurring. In the data I see more C ...
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2answers
69 views

What are “+” and “Ar” in consensus binding sequence of amino acids?

So I was reading this paper and found a figure as below: I understand that [LEAM] means any of LEAM residues, pS is phosphoserine and X means any amino acid residue. What is [+] here ? Is both R and ...
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0answers
59 views

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 ...
3
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2answers
890 views

difference between motifs, domains, patterns, signatures and profiles

I can't get clear the difference between those terms, I see them a lot while browsing on Prosite, Pfam, Expasy e.t.c. However, I can find documentation about them, but It still not clear what the ...
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1answer
95 views

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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3answers
3k 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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1answer
2k views

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. ...
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3answers
517 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 ...
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1answer
269 views

How do high-throughput/NGS sequencers calculate quality scores?

I am confused as to how quality scores are actually calculated by DNA sequencers like Illumina. For each base call, some quality predictor value is computed, based on various properties of the ...
6
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1answer
825 views

What is the biological significance of k-mer counting?

There are many tools developed to compute the counts of k-mers present in a gene sequence. Jellyfish, Bloom Filter Counter, DSK Kmer Counter, KAnalyze, KMC 2 etc are some efficient software developed ...
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1answer
75 views

Which is the proportion of metagenomics reads that cannot be mapped in any genome?

I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable? I found a figure for viromics, which seems ...
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2answers
648 views

Basic Genotyping

As a disclaimer, I'm from a computer science / statistics background, working on some bioinformatics problems. I've got some genotyping data (VCF from Exome Sequencing), and I'm struggling to get my ...
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2answers
1k views

Fold Coverage of sequence read? [duplicate]

What does it mean when N-Fold coverage of read of sequence? Details will be much appreciated if a link provider with brief explanation.