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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16
votes
2answers
17k 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 softwares, but varies from software version to version. ...
9
votes
1answer
165 views

Comment on the introduction to a bioinformatics paper

I've written a paper about DNA sequence analysis. This paper attempts to use Bayesian modelling for a set of DNA sequences. It will probably end up either in a statistics journal, or, more likely, in ...
7
votes
2answers
465 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 ...
7
votes
1answer
80 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 ...
7
votes
0answers
59 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 ...
6
votes
2answers
77 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: ...
6
votes
2answers
72 views

Predicting and identifying microbes and enzymes DNA sequence with metabolic prediction

Presently I am working on metagenomics of coal biomethenation by bacterial consortium. I have got the sequence result (Illumina). The sequence is huge and I can't predict anything from the sequence. ...
6
votes
1answer
72 views

(Rough) Model for DNA evolution in E. coli genes

I need a model of in-gene DNA drift. I'm not interested in bacterial phylogenies alone. Here is what I understand: Sequences corresponding to genes have both exons and introns, but in bacteria the ...
5
votes
1answer
318 views

Where can I find the pMON7124 plasmid sequence?

I need the map of the pMON7124 plasmid. As this is not easy to find, I welcome any hints.
5
votes
1answer
208 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 ...
5
votes
1answer
101 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 ...
5
votes
3answers
494 views

Tool for nucleotide alignment with all nucleotide codes (e.g. R, Y, W, S, etc.)?

I have a vector sequence and would like to find the following nucleotide sequence in it. AASYWSRA This query sequence uses several degenerate symbols, defined ...
4
votes
4answers
405 views

Is there a PSI-BLAST for nucleotide sequences?

I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs ...
4
votes
2answers
224 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 ...
4
votes
1answer
226 views

Blosum matrix with probabilities instead of the positive and negative scores

I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like ...
4
votes
2answers
124 views

Reference sequence for defining single nucleotide polymorphisms

Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in ("dbSNP—Database for Single ...
3
votes
1answer
664 views

Ka/Ks (dN/dS) analysis module for Python?

From this wiki article: In genetics, the Ka/Ks ratio (or ω, dN/dS), is the ratio of the number of Nonsynonymous substitutions per non-synonymous site (Ka) to the number of synonymous ...
3
votes
1answer
196 views

Any tool to align whole genome sequence data to another genome and give exon regions a higher mark?

I want to align WGS data from several mammals to one reference such as the human genome sequence. Since in most cases exons should be conserved and spliced in the same way and introns should vary, I ...
3
votes
1answer
680 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 ...
3
votes
1answer
862 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 ...
3
votes
1answer
57 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, ...
3
votes
0answers
44 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 ...
3
votes
0answers
93 views

Data analysis of transcriptome sequencing data [closed]

I want to learn more about the data analysis and statistics on transcriptome sequencing data. I would like to read some important papers of the field and books and maybe some MOOCS, if they are ...
3
votes
0answers
136 views

Good poly-A filtering rules or tools

I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have ...
2
votes
2answers
86 views

Change Genbank entry date with Biopython

I can create a new Genbank record in Biopython with the following code: ...
2
votes
6answers
275 views

Sequence analysis software suites

I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what ...
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
votes
1answer
103 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, ...
2
votes
1answer
144 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?
2
votes
2answers
62 views

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 ...
2
votes
2answers
79 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 ...
2
votes
1answer
85 views

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 ...
2
votes
0answers
71 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
vote
1answer
63 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 ...
1
vote
2answers
29 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
1
vote
2answers
57 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
vote
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?
1
vote
2answers
108 views

Recommended sequence clustering algorithm for transcriptome data

I'm working on a project where I'm going to analyze a large amount of transcriptome data. After assembling our RNA-Seq reads into contigs using Trinity, it looks like I'm going to have about 10GB of ...
1
vote
1answer
289 views

Codon alignment via Python? [closed]

I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process. So far.. I retrive pairs of orthologous DNA sequences from ...
1
vote
2answers
133 views

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 ...
1
vote
1answer
49 views

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 ...
1
vote
1answer
123 views

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 ...
1
vote
1answer
93 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 ...
1
vote
1answer
43 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 ...
1
vote
1answer
55 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

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, ...
1
vote
1answer
50 views

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 ...
1
vote
1answer
212 views

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 ...
1
vote
0answers
26 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 ...
1
vote
0answers
23 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 ...