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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17 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. ...
2
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4answers
82 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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0answers
12 views

Finding SNPs and Haplotypes?

I have the following alignment file. How can I identify the SNP sites and how can I find the haplotypes. I know these are related but can't seem to apply it to the below data. Any help would be ...
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1answer
42 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 ...
4
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1answer
55 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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0answers
8 views

What's the regulation of natural antisense transcripts?

By running an in silico approach on TF binding site prediction, I've discovered binding motif similarity on a nucleotide sequence within the EGFR-AS1. I was quite surprised, given that the ...
3
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1answer
45 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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2answers
50 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.
0
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1answer
30 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
63 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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1answer
44 views

curly braces in sequence motifs

what do curly braces in sequence motifs stand for? e.g. in RTCRYBN{4}ACG what is N{4}? moreover, i notice that in TRANSFAC ...
6
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2answers
138 views

Why is the quality range of fastq format so broad?

Referring to fastq format, it is clear that in fastq format, there are 94 quality value for a sequenced Nucleic Acid of a DNA sequence read and they are: ...
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0answers
11 views

Which ScoreMatrix and GapPenalties should I use?

I'm a Software Engineering student, and I'm dealing with a Sequence Analysis problem. The problem is the following: Find phenylalanine hydroxylase of at least six different species, then perform a ...
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0answers
93 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 ...
7
votes
1answer
91 views

How can I generate a random DNA sequence?

I've found this paper which involves the construction of 19-bp random DNA sequences, but I don't know enough biology to understand how this method works. Could someone explain it to someone who is ...
1
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1answer
64 views

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 ...
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0answers
37 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 ...
2
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2answers
32 views

Where I can download the genome sequence of various species of Fusarium?

I'm looking for genome sequence of various species of Fusarium (a kind of fungus!) on net, but I found no suitable information. Could you please help me out for this purpose? Thanks in advance
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2answers
103 views

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 ...
1
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1answer
46 views

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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0answers
26 views

Batch several sequences for absent restriction sites

I have a collection of about 120 7kB sequences I would like to check for ether a list of specific restriction sites, or what restriction sites might be absent in all of them. Is there a app or ...
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0answers
31 views

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 ...
0
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0answers
26 views

Walkthrough Analyzing/Processing Genotyping Data for Association Studies

I need help outlining the data analysis process of analyzing genotyping data you get back from a Next Generation Sequencing experiment. Here are the steps I currently believe you go through, but I ...
1
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0answers
58 views

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 ...
0
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2answers
115 views

What do Illumina HiSeq/MiSeq paired end reads look like?

My understanding is that paired end reads from the Illumina HiSeq/MiSeq platforms looks something like this: R1: AAAAAACCCCCC R2: GGGGGGTTTTTT Where the ...
2
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2answers
89 views

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 ...
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2answers
46 views

Properties that can be derived from amino acid sequences [closed]

What are the properties that can be derived from an amino acid sequence apart from those mentioned in the website? In the mentioned website, the properties that can be calculated from amino acid ...
0
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1answer
33 views

Marker validation using transcriptome and genomic sequences derived from a single cell

I conducted a SSR marker analysis using bioinformatic tool on some RNA-seq data of human tissues. Now, my supervisor believed that we have to validate these SSR on a transcriptomic and genomic ...
3
votes
1answer
79 views

Is sequencing error a function of the nucleotide being read?

Checking out on Google Scholar, I can see that for Illumina (just to consider one example) the sequencing error rate is of the order of 0.001-0.01 per nucleotide. Talking about sequencing error, ...
2
votes
1answer
73 views

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 ...
2
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2answers
111 views

Change Genbank entry date with Biopython

I can create a new Genbank record in Biopython with the following code: ...
2
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0answers
77 views

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 ...
1
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1answer
107 views

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 ...
0
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1answer
77 views

What does the “cov” mean in a velvet assembler generated contig name?

A exmaple of a contig name generated by velvet assembler: NODE_127_length_39203_cov_244.873016 What does cov_244.873016 mean? ...
1
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1answer
44 views

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 ...
6
votes
1answer
236 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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0answers
68 views

How do I select the sequence identity threshold in cd-hit to cluster proteins for core genome comparative analysis?

Can anyone suggest a method for selecting the sequence identity threshold for protein clustering in cd-hit? If I use too high of a threshold, then the number of protein clusters shared between three ...
0
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0answers
15 views

Why low variant frequency in exomeseq data (ANNOVAR)?

I've got an annotated ANNOVAR file with 300.000 nucleotide variants of 4 genomes. There's one thing I don't understand when looking at the data: Why are the variant frequencies so low in comparison to ...
0
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1answer
40 views

What does a read simulator do?

There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software
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2answers
34 views

Ribosomal DNA references sequences

I'm having a bit of trouble with searching for this piece of information. I'm doing a study related to phylogenetic susceptibility of hosts to pathogens (based on a recent Nature publication), ...
3
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0answers
48 views

How can I create R8 (homopolymer repeat) filter without using illumina pipeline?

illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and ...
0
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0answers
77 views

Demultiplexing symmetric PacBio reads

I have PacBio CCS.h5 and the corresponding fasta and fastq files and I would like to demultiplex them. Does anyone know of how this can be done in the absence of bas.h5 files. Thanks for your help! ...
5
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1answer
123 views

How do biologists infer correct ORF of a DNA sequence?

Each DNA (RNA) sequence has 6 possible Open Reading Frames(ORF). My question is: What are the theoretical bases of in vitro or in silico tries to find correct reading frame of a sequence? Is it just ...
0
votes
1answer
102 views

How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis

I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be ...
2
votes
1answer
115 views

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, ...
1
vote
1answer
56 views

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 ...
1
vote
1answer
59 views

Testing monophyly from per site log-likelihoods without optimising branch lengths

How can I obtain per site log-likelihoods for a topology against an alignment without optimising branch lengths? (which software can I use to do this) Per site log-likelihoods can be used for various ...
3
votes
1answer
828 views

Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?

Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge ...
0
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1answer
29 views

genomatix software linux install [closed]

I have installed the genomatix software which is a jar file the name is InstallChipInspector21.jar.But now I really don;t know how do I start it ,can any one suggest me a method??
7
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2answers
567 views

RNA-Seq library construction challenges: the biases of RNA fragmentation vs cDNA fragmentation

I recently watched a presentation on RNA-seq that covered some of the choices one can make along the way, and I didn't fully understand one of the choices in particular. Near the beginning of the ...