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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2
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1answer
16 views

Determine if two molecule structures are the same molecule (perhaps in different conformations)?

I have two .pdb files describing two (small ligand) molecular structures. I need to determine if these two pdbs describe the same molecule, perhaps in different spatial conformations. Is there a ...
0
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1answer
16 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 ...
0
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0answers
23 views

What the definition of a flanking residue? [on hold]

What the definition of a flanking residue? How do you define whether an amino acid is flanking or not? What are the environmental or physiochemical conditions in which a residue is considered to be ...
0
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1answer
23 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 ...
2
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0answers
21 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. ...
2
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1answer
38 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
42 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 ...
1
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1answer
44 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: ...
0
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0answers
16 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 ...
0
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0answers
18 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 ...
15
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1answer
487 views

Additive genetic variance components from LMER in R

I've set up some dummy data in R which makes 40 genetically related lines, they are all siblings within a line so are genetically related by a factor of ½ thus additive genetic variance should be ...
0
votes
1answer
25 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 ...
2
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0answers
56 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 ...
0
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0answers
31 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 ...
0
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2answers
62 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 ...
2
votes
1answer
21 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 ...
5
votes
2answers
94 views

Do variant callers miss rare variants in reference?

Generally variant calling programs (such as GATK-UnifiedGenotyper) look for differences between reference genome and submitted sequence. However, we all know that reference genome consist rare ...
0
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0answers
9 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 ...
1
vote
1answer
50 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 ...
0
votes
1answer
29 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 ...
2
votes
1answer
57 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 ...
1
vote
3answers
67 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 ...
10
votes
2answers
913 views

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

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns ~146,000 proteins. I was under the impression that there were only 20-25,000 proteins in ...
1
vote
1answer
86 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. ...
1
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1answer
51 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 ...
8
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6answers
424 views

Introductory literature for synthetic / systems biology?

I'm a computer engineer (MsC Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I've got a comprehensive layman's understanding of evolution, genetics, ...
1
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0answers
52 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 ...
7
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2answers
133 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, ...
0
votes
1answer
28 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 ...
4
votes
1answer
140 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
3
votes
1answer
42 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 ...
12
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3answers
1k views

Databases for gene regulatory network graphs?

What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported ...
0
votes
2answers
117 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
votes
1answer
44 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 ...
1
vote
1answer
42 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 ...
12
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2answers
115 views

How can we verify predictions of protein folding in silico?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
0
votes
1answer
31 views

How reliable is SwissProt topology?

I am using TOPO_DOM annotations from uniprot databases to characterise the orientation of transmembrane features. Is SwissProt topology experimentally validated, ...
13
votes
2answers
11k 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 ...
0
votes
1answer
35 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. ...
4
votes
1answer
29 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) ...
2
votes
1answer
48 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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0answers
40 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 ...
3
votes
0answers
52 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 ...
11
votes
0answers
131 views

Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

I experience big discrepancies when calculating melting temperature of RNA 7-mers with Biopython over values generated by a popular algorithm. I tried the nearest neighbour algorithm with RNA and ...
0
votes
2answers
77 views

Programmatic way to differentiate homodimers from heterodimers?

For pdb files is there a simple programmatic way to determine if the file is made up of homodimers or heterodimers. I have many files so an online tool or some ...
1
vote
2answers
63 views

What's read depth in VCF?

There is an attribute defined as DP (Total Depth) in VCF file format. For example, http://www.1000genomes.org/node/101. What does this attribute mean? If I get a value of like DP=128. How can be that ...
3
votes
2answers
48 views

Deciding a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset

Is there a methodology to select a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset, to define when there is a significative alteration? Can I download CNV data for ...
-1
votes
1answer
47 views

What is enrichment? [closed]

Could someone please clarify, in layman's terms, what enrichment means? I'm currently looking at MACS and peak calling. Repeated mentions of "enriched" or "enrichment". Thanks.
-1
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3answers
47 views

Patterns/Motifs Repository [closed]

I am new to this area. I am a researcher working on fast pattern searching in general scenarios (e.g., regex in string matching). I am curious about the "regular expression (regex)" (pattern/motif) ...
1
vote
1answer
114 views

best book for a comprehensive introduction to biology for a computer science graduate interested in undertaking research in bioinformatics [closed]

I have a postgraduate degree in computer science, and I wish to undertake research in bioinformatics. I had chemistry but no biology in high school. I have read bioinformatics books like "biological ...