Bioinformatics connects life sciences and quantitative sciences, typically involving the application of software and algorithms to solve computationally intensive questions, such as those in genomics, sequence analysis, and systems biology. Questions tagged Bioinformatics should have a direct ...

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102 views

How to find a Cancer PPI network data [closed]

I need a Protein Protein Interactions network of Cancer (any type - just I want a PPI of any type cancer), I search and see DIP PPI and .... How to specify that is Cancer PPI and how to get a PPI of ...
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1answer
70 views

How to interpret the simple sequence repeat (SSR) on the coding sequence, but not the related protein sequence?

I have predicted some SSR repeat on the gene of interest using SSRLocator program, which the result creates a question for me. Please consider the below sequence, which is part of gene sequence of ...
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3answers
548 views

What is the biological significance of finding palindromes in DNA sequence?

I found a function called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of ...
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1answer
54 views

blastn: What substitution matrix is used?

I'm currently working aligning sequences, and I need to compute similarity between pairs of DNA 'words' of a particular length. For amino acids I am able to use the substitution matrices in Biopython ...
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2answers
57 views

How can I find some pieces of the genome of a microorganism?

I have figured out how to download the fasta of the genomes of microorganisms, for example the botulism bacteria and the spirulina algae. However, I want to find a fasta file for some significant ...
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142 views

Normalised gene counts to edgeR/DESeq2?

Both very popular differential expression packages assume a raw gene matrix count. This makes sense because the statistical model models the library depth. But what if I normalize my counts with say, ...
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1answer
55 views

Expected dS/dN ratio for exome

I am trying to determine whether or not my sequencing data has more/less non-synonymous mutations than would be expected. My understanding is that there is some fixed ds/dn ratio for the human exome ...
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61 views

Is studying complete mitochondrial genome need biological lab work?

The research complete mitochondrial genome study done on species: Juema pig Sus scrofa (Suina: Suidae) from southern Gansu red rainbowfish speckled dace, Rhinichthys osculus white char Salvelinus ...
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4answers
230 views

How to convert FASTQ file format into GTF file format?

I have a plenty of FASTQ files (FASTQ is a standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer) and need to convert them to GTF format (gtf - ...
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1answer
144 views

What is the last heavy atom of an amino acid?

I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it ...
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1answer
92 views

difference in genetic instuctions between male and female [duplicate]

I'm a computer science graduate so please bear with me the following computer program : mov ecx, -1 INC ecx consist of 2 instructions (mov,inc) each working on specific data , can genetics ...
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0answers
99 views

How to interpret this cuffcompare result? Sensitivity over 100?

I run a cuffcompare: cuffcompare -r transcripts.gtf TransStandard_1.0.gtf I got the following result: ...
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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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1answer
53 views

Why the length of UTR in the genomic sequence of gene X is too much longer than the same region in the corresponding Refseq mRNA sequences?

I'm browsing in the UCSC genome browser and found that the UTRs length of KIAA0040 gene in the genomic sequences is too much longer than the corresponding the Refseq mRNA sequence. In fact, the total ...
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1answer
63 views

What is difference between several mRNA RefSeq for one gene?

I'm looking for mRNA RefSeq sequences for a given gene in the UCSC genome browser by searching gene name "HLA-F" in human (scroll to Refseq genes section). There are several RefSeq mRNA for the gene, ...
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2answers
232 views

Plot coverage per base for BAM file

I have a BAM file and a BED file for my own chromosome. I would like to get coverage per base and ideally construct a histogram of coverage across each gene. The motivation is to visualise the ...
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37 views

Bioinformatics - DNA binding, sequence-specific protein data

I am a computer scientist and we are working on protein function prediction algorithms. Right now, we would like to examine protein-DNA binding properties computationaly. For this, we would make use ...
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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 ...
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1answer
99 views

Why perform imputation?

Genetics datasets contain measurements for millions of single nucleotide polymorphisms (SNPs). Some (usually small) percentage of these values are of low confidence, and are labeled as missing values. ...
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1answer
104 views

Differential gene expression analysis between species

I have RNA Seq data from mouse and human skin ( 2 replicates each) and want to compare the expression of the orthologous genes to find any which are differentially expressed. I have quantile ...
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0answers
45 views

How does the brain store information? [duplicate]

In all electronic devices with the possibility of saving there are tiny magnets that can store your data by the state they are in. In general, there has to be something changed to store information ...
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2answers
126 views

Construct Phylogeny form Edgelist

I am working on large scale biodiversity simulations and have collected a lot of data on simulated phylogenies. I have a list of child-parent edgelist species in the form: ...
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119 views

How to model missing residues on a protein from multiple PDB files?

I have multiple X-ray structures (PDB files) of the same protein. All of them have missing stretches of residues. I want to use all of them to build a single model, with as little missing residues as ...
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32 views

Normalise protein database domain-wise

Suppose we've collected a big (hundreds of thousands) library of different protein sequences with certain features. Then we want to use this data base to train a classifier. And for several ...
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1answer
35 views

E value cutoff for RNASeq search

I am trying to narrow down the possible search criteria from an RNASeq experiment. I already have the cds sequences so I took these and used Blast+ program to blast the data against itself to find ...
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0answers
67 views

Do mutations come in pairs? [closed]

As DNA is organized in a double-helix, a change in one strand must be accompanied by a corresponding change in the other strand. Let's say an original sequence CATCAT mutates into CATGAT. The other ...
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80 views

How to get Population Genotype Frequency from 1000 genomes Perl API

Posted a similar question on Biostars but got no response. Not sure if I'm allowed to link to it? Basically I want to pull genotype frequency data for a population group (such as CEU) instead of ...
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2answers
72 views

Molecular graphics

anybody know of some great free molecular graphics systems that can allow for PDB code input? I prefer that it doesn't use Java. I also prefer that it is online, although if there is a great system ...
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1answer
44 views

Is there a good site or software to see if a primer pair spans an exon junction?

I am going to perform some RT-qPCR tests to validate an experiment.  I'm currently in the process of ordering primers, and I would like to get them from the Harvard Primer Bank since these have been ...
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15 views

What is the best aCGH normalization procedure for hyper-ploid tumor samples?

I'm currently working on aCGH data of Triple Negative Breast Cancer patients xenografts and primary tumor samples. A substantial amount of my samples is highly aberrated which leads to offsets of the ...
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1answer
47 views

What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way?

First post here, so bare with me if I violate any etiquette or formatting rules. Let's say I've got a protein in humans. When it interacts with an ncRNA found in humans, it does something that I'm ...
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1answer
539 views

What is the strand specificity of a reference genome?

It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue. So here's ...
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3answers
391 views

Merge several .ab1 sequence files into a single FASTA file?

I have several .ab1 files generated from Chromas. I want to merge all of them into a single FASTA sequence file. How can I do this in an automated way? Note that I don't have Chromas installed (the ...
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1answer
104 views

A tool to get annotation features by position in the reference genome

Previously, when I needed to find a genomic feature (promoter, CDS, repeat etc) that underwent mutation (SNP) I used my own scripts to load an annotation file, parse it, map the SNP's position and ...
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2answers
1k views

Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
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1answer
263 views

IC50 calculation [closed]

I am a computer science student and I'm in an internship at a genomics and biotechnologies research institute. My current task is to calculate the IC50 and the EC50 given a set of data as a table. ...
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1answer
89 views

How to compare two RNA transcripts?

In this paper, the cuffcompare RNA package is reported: Because of the stochastic nature of sequencing, assembly of the same transcript in two different samples may result in transfrags of ...
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1answer
75 views

Primer Design with Primer-BLAST over specific site

I am trying to design primers using Primer-BLAST such that the forward primer spans a specific base pair site. I am looking at KRAS for which I believe the RefSeq ID is NG_007524.1 and the forward ...
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0answers
163 views

Interpretation of qPCR results for low expression genes

I am attempting to validate existence of a transcript using 40 cycle qPCR. I designed primers for a unique feature of this transcript, and also designed primers for a sequence in the transcript that ...
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1answer
44 views

What does “each pathway define an independent genotype” mean?

In a section of this paper. However, if the question of independency is posed in the form: “Does each pathway shown define an independent genotype?,” then each of these three pathways is ...
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1answer
73 views

Are there journals for theoretical models of protein-protein interactions?

Are there respectable scientific journals for publishing models of protein-protein interactions obtained by docking simulations? I would also discuss the biological significance of the particular mode ...
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2answers
207 views

What are some (bioinformatic) methods to characterize potentially novel gene transcripts?

I am working with a few novel transcripts of genes- before I confirm their existence experimentally, I would like to perform some bioinformatic analysis. I have already considered coding potential, ...
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2answers
925 views

What are the programming languages important to learn for a geneticist or bioinformatician? [closed]

I am interested in learning more about both genomics and bioinformatics, with emphasis on genomics. I was told after taking an introductory course of genomics that the programming language "R" and ...
2
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1answer
49 views

Hodgin-Huxley model for a single neuron - continuation

As continuation to This question I have posted. Another set of questions is given for the same model : This time it is also given that for $t<0$ the membrane potential is $u_0$, and at $t=0$ it ...
2
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1answer
113 views

Extract protein sequences from a GBK(GenBank) file without scripting [closed]

How to extract protein sequences from a GBK(GenBank) file without scripting? I know that writting a script using BioPerl or Biopython can do this, but it is not elegant and daunting to beginners and ...
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1answer
36 views

What is the difference between options protein and replication in the NCBI database?

After checking the NCBI help page, I am still unclear about the difference between protein and replication interactions for HIV. ...
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0answers
79 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 ...
3
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1answer
42 views

Which hydrophobicity scales are best for detecting transmembrane regions, and why?

There are many hydrophobicity scales for protein analysis. Broadly, I gather the differences between them are from the experimental method to acquire the data and the normalisation (or lack thereof) ...
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0answers
121 views

Cut-off values for LD, LOD and D-prime as algorithmic input

I created an algorithm to generate SNPs for random people of different descents - based on HapMap data. While this works good, there is something else I want to take into consideration. So if a SNP ...
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1answer
109 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 ...