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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20 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 ...
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1answer
24 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 ...
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1answer
21 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? ...
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1answer
34 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 ...
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1answer
52 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 ...
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2answers
10k views

What is the difference between local and global sequence alignments?

Obviously 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 differs from software version to version. I am aware that ...
5
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1answer
130 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
12 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 ...
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5 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 ...
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1answer
34 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
28 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), ...
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0answers
24 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
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1answer
173 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 ...
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34 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
56 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 ...
4
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2answers
172 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
59 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 ...
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1answer
80 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, ...
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4answers
311 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 ...
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1answer
51 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, ...
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1answer
35 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
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1answer
288 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 ...
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1answer
156 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 ...
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1answer
24 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??
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2answers
226 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 ...
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1answer
113 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 ...
5
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1answer
206 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.
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1answer
44 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 ...
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2answers
52 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 ...
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2answers
88 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 ...
2
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1answer
94 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?
4
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1answer
123 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 ...
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1answer
49 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 ...
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0answers
120 views

Is the default kmer 25 value in Trinity still ok for assembly of 150bp reads from Illumina HiSeq 2500?

I will soon be receiving Illumina HiSeq 2500 data (150bp PE stranded reads). In the past we have been using Trinity as our assembler of choice, but it uses a default kmer value of 25. I believe this ...
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6answers
231 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 ...
3
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0answers
90 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 ...
2
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1answer
549 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 ...
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2answers
98 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 ...
4
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2answers
109 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 ...
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1answer
205 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 ...
3
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1answer
533 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 ...
2
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1answer
61 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 ...
3
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0answers
126 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 ...
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1answer
187 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 ...
5
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3answers
403 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 ...
6
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2answers
70 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
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1answer
71 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 ...