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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1answer
192 views

How does one calculate the amount of oxygen produced by trees?

I'm currently working on a project to measure the impact of tree planting. Calculating the amount of oxygen seems harder than I imagined. Of-course there's the type and size of the tree and the ...
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2answers
61 views

yeast protein secondary structure

i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous ...
4
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1answer
165 views

How do I make a multiple sequence alignment (MSA)?

I have a DNA sequence that makes protein 1, but now I have asked to: compare the amino acid sequence of protein 1 with nine homologous proteins and make a multialignment of the sequences. Determine ...
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2answers
39 views

Data Retrival from the GenBank?

When I go to NCBI & Select nucleotide option there and in search box write For Example CNGA3 gene the page shows that there are 553 items.I know the method of downloading or retrieving the One ...
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0answers
67 views

How do you create a .snp datafile?

I'm looking to use the software DIYABC 2.1.0 to apply approximate bayesian computing (ABC) to some resequenced data that I have. The resequenced data is in FASTA format however, and the software ...
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0answers
27 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 ...
3
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1answer
60 views

How to predict a mRNA secondary structure with a large sequence?

When I use some web servers to predict a mRNA secondary structure, I find they always required in a small size sequence. If I use a long sequence and cut it into small parts, do these small parts ...
2
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1answer
36 views

Why my base-quality in alignment is not perfect?

I have a fasta file with some DNA sequences. I would like to simulate next-generation sequencing reads from it. I'm doing it without any base error and mutation error. ...
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0answers
40 views

Shortest path and influenza spread

I have been researching on the applications of the shortest path problem to biology. I thought about modelling the spread of influenza virus and wondering if there was previous research on the topic. ...
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0answers
25 views

NCBI EUtils. Get Homolog infromation using Gene ID

How to retrieve homologs information in xml or json format from NCBI using gene ID? I tried one URL: ...
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1answer
13 views

num_tol_term in PeptideProphet result

What is the meaning of the num_tol_term attribute in a PeptideProphet (pep.xml) search_hit? ...
3
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2answers
151 views

Is there a database of cell images?

We're working on an algorithm for processing images of cells, similar to but much more basic than Cell Profiler, and we are looking for a large database of cell images to test our software. Can anyone ...
2
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1answer
85 views

What is biological intuition?

Whenever I read or learn about prediction tools or aligners or motif detectors, I also hear that they are lacking in something called biological intuition. But I haven't been able to find a solid ...
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0answers
42 views

What program was used to create this visualization of a neighbor-joining tree?

I know there are many programs out there to visualize neighbor-joining trees in phylogenetics. I have a tree in Newick format. Does anyone recognize the features of this image as coming from a ...
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0answers
81 views

How to identify a pseudogene to a specific protein coding genes?

Pseudogenes are those sequences in the genome that bear similarity to specific protein coding genes, but nevertheless are unable to produce functional proteins due to existence of frameshifts, prema- ...
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2answers
134 views

Do the bacterial species X, Y, Z code for proteins A, B, C?

My PI has assigned me a task to gather evidence to determine whether or not a list of particular species of Campylobacter and Helicobacter code for a list of several proteins. To put it simply I’ve ...
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1answer
106 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
71 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
649 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 ...
3
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1answer
57 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 ...
0
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1answer
159 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, ...
0
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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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1answer
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
249 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 - ...
3
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1answer
162 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 ...
0
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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 ...
2
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1answer
123 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
93 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
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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
66 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
278 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 ...
0
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1answer
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 ...
0
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1answer
34 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
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1answer
103 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
113 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 ...
3
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2answers
132 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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0answers
123 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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0answers
34 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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1answer
37 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
68 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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0answers
90 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
75 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 ...
1
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1answer
45 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 ...
0
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0answers
16 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 ...
0
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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 ...
2
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1answer
650 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
428 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 ...
1
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1answer
107 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 ...