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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Measuring tumor heterogeneity [closed]

I would like to ask if there's any method (established or not) in order to quantify heterogeneity found in mutations occuring in primary neoplasms and metastatic lesions (either common or private) and ...
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1answer
57 views

How can I obtain a computer readable model of Dr. Gerhard Michal's biological pathways map?

I want to run simulations of various metabolic pathways – the project could end up becoming quite large, and having a machine readable chart would make thing a lot easier. Does anyone know if there is ...
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37 views

Get Parent GO terms of GO term vector?

I have a vector of GOIDs that are specific GO IDs outputted from an enrichment analysis. I want to cluster my GOIDs by their parent GOID term. I used GOstats to do my enrichment analysis, and I have ...
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1answer
54 views

Data on Gene Position in Human Genome

I am trying to get some data on gene position in the human genome and I need some help What I tried I downloaded ...
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35 views

How to construct tumor phylogenetic tree?

I would like to know if anyone has tried any software that constructs tumor evolution trees where the trunks represent the common mutations and the private alterations are noted on each branch. I can ...
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38 views

Extracting the donor/acceptor sites from mRNA sequence(PERL/ DNA transcription)?

I have the following program that I am analyzing and trying to understand. Overall purpose of it is to put out, based on the option selected, the set of introns, exons, acceptor sites , or donor sites ...
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47 views

Data on Recombination rate and Gene Positions in Humans

I am looking for estimates of per base pair recombination rate in humans and indication on gene positions. The goal is to be a able to plot recombination rate in the y-axis and position (in bp) along ...
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3answers
74 views

DNA to Binary Distance Computation [closed]

If I represent DNA as binary values, what is the best way of computing distance between them. So : A = 00, T = 11, G = 01 and C = 10 Hamming Distance between ATGC and TAAC is 3, however their ...
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1answer
52 views

How many paraphyletic groups can be formed from a phylogeny?

How many paraphyletic groups can theoretically be created from this phylogeny? I found (2n)-2. Is this correct? This is not homework nor exam, just a question about paraphyletic groups.
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92 views

Why do we encode information in DNA in binary and not in base 4?

I recently read an article about Harvard scientists encoding 700Tb of data in DNA strands. But they encoded the information in base 2, so T and G was a 1 and C and A was a 0. But why binary? Why didn'...
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40 views

How do I retrieve electronic annotation from Uniprot and GO records that relates to molecular function?

I'm interested in the endonuclease activity of the G3BP1 gene, specifically the uniprot record Q13283. An external link guides me to UniprotKB-KW electronic annotation. How can I retrieve valuable ...
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2answers
62 views

Grouping OMIM disease codes

I have ~100 sets of genes, and each set includes between 2 and 70 genes. I'd like to perform an enrichment analysis on each of these sets to test if they're enriched for OMIM disease labels. However, ...
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17 views

What is the best test for SNV clustering?

I am looking for a method to cluster single nucleotide polymorphisms based on clinicopathologic data (mainly receptor immunoistochemistry). So far, I've came up with only two that handle dummy ...
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2answers
65 views

how to compare Smith–Waterman algorithm implementations?

Assume that you have two softwares of smith waterman algorithm (with what ever heuristic they apply to speed up) for local sequence alignment of genomic sequences. I would like to know if for sure ...
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0answers
25 views

Gene expression data [closed]

I am using gene expression data for the classification of cancer. I need to know how the values are processed. within what range the values will be? What does the negative value means? How can I do my ...
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25 views

Predicting alternative transcript sequence and probability from a single SNV

I am currently studying a small number of non coding SNPs in terms of their contribution to the cancer phenotype. All are obtained from massive parallel sequencing on a specific gene panel, utilizing ...
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2answers
77 views

How to predict the effect of a non coding SNP variant on the expressed protein?

I am writing a paper for non coding SNPs on patients with metastatic breast cancer. Having used a specific gene panel (NGS) of approximately 60 genes, I'm currently running out of ideas on what to ...
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1answer
48 views

Are there any major noticeable limitations to genome sequence compression methods that use reference templates?

Recently, I have been researching about big data analytics in biochemistry, and started wondering about how genome sequence compression could affect analysis. Of all the method listed on the ...
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0answers
15 views

Trouble identifying a gene given an Expressed sequence tag

I have an assignment where we need to answer several questions about an EST, however, I'm having trouble getting started. My sequence contained a Not I site (clipped that) and no poly A signal. We ...
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2answers
57 views

Fold Coverage of sequence read? [duplicate]

What does it mean when N-Fold coverage of read of sequence? Details will be much appreciated if a link provider with brief explanation.
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1answer
71 views

Why does BLAST employ local alignments? [duplicate]

Why does BLAST use Local alignment, not Global alignment? And when would a global alignment be useful?
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1answer
55 views

Bioinformatics basics [closed]

What are the basic differences between genbank, NCBI and entrez gene? And please tell some books and webpages where I can get more about the databases .(currently I'm using Bioinformatics and ...
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1answer
52 views

How do I measure genetic distance?

I'm not sure how to measure genetic distance. There seems to be many different equations out there, and all the ones I found are rather old. In my specific problem I want to see if the twist in ...
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0answers
66 views

How can a medical doctor use the information given by someone working in medical image computing(shape analysis)? [closed]

Sorry for the long headline! In short, I'm an academic researcher working in an area called "statistical shape analysis", which is intimately connected with medical image computing. It deals with how ...
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15 views

Format for background [closed]

Usually, after people finish an experiment. They will do a report. What do people need to write for background. Do people need to write the concept this experiment need or just explain briefly about ...
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21 views

Cell specificity RNASeq [closed]

I am working on finding the cell specifity information (eg. Epithelial cells, muscle cells etc) from RNASeq data of colon tissue. I was referring to CellCODE but that is related to PBMCs. Does anyone ...
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1answer
45 views

Accessing Expression Levels for Genes of Interest from GEO Experiments

I have a list of 100 lncRNAs (long non-coding RNAs). For each of these RNAs, I would like to query GEO to find any experiments that used a high throughput sequencing platform and detected expression ...
3
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1answer
48 views

constitution of read and gene region (IGV)

I work with fastq files containing NGS reads for some human DNA regions. The reference genome is hg19. I had two fastq files (pair-ended). I generated alignment BAM files. I used "bwa" and samtools to ...
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2answers
58 views

What tool to use to map reads (samtools, sequencher,…)?

I am a beginner in Bioinformatics. I have 4 files: 2 fastq files (aln1.fastq and aln2.fastq) 2 bam files (aln.bam and aln.bam.bai) I know that: the raw file is aligned to hg19 human genome. The ...
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2answers
112 views

Is it possible to create a restriction map using python? [closed]

I have some fragments of DNA from single and double digests using three different restriction enzymes. I'm trying to construct a restriction map of a linear fragment of DNA. The map needs indicate the ...
4
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1answer
102 views

How to get the correct RefSeq Protein transcript for a given RefSeq Nucleotide transcript?

How to get versioned Protein Accession Number for a Refseq Accession Number? I have some versioned RefSeq Accession numbers and I would like to know their corresponding Protein Accession Numbers. ...
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48 views

Pairwise sequence alignment in C++ (fastq et bam) [closed]

I am sorry I am a beginner in genetics and I have a problem about a homework project. I have 4 files: aln1.fastq aln2.fastq aln.bam aln.bam.bai "fastq" files contain information about sequences ...
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1answer
28 views

Tool for translating chomosome, index numbers to sequence information

Is there a tool which allows me to transform information in the form (chromosome number, start index, end index) to sequence information? For example, something like (6, 43770819, 43770841) should ...
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29 views

DNA binding Domain [closed]

How to say whether a specific amino acid in a protein is binding to DNA or not from sequence alone and what are the features or characteristics to be considered?
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0answers
32 views

how to visualise a network of proteins complex? [closed]

I would like to know how to visualise a complex of several proteins lets say I have a list of proteins ...
6
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1answer
112 views

How can I make a protein interaction/protein-complex network?

Let's say I have a list of proteins ID. I would like to know whether I can find any complex based on that list. Any example, explanation is appreciated. An example input is what you see below. What ...
3
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1answer
63 views

Understanding common identifier codes (IDs) in biology databases

I know this is very basic but I would like to understand it and it's difficult to know where to begin with a new database. I have the output: ...
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0answers
35 views

How many residues can a reliable ab initio structural model contain?

A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be ...
4
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2answers
100 views

What are sources for learning bioinformatics for self-learning?

What are the sources for learning bioinformatics(books, websites/MOOCs)? Does it require prior knowledge of programming language because I am a complete noob when it comes to programming language.
4
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1answer
34 views

Choice of Molecular markers to carry out molecular phylogenetics

For evolutionary analysis of different individuals within a population, the preferable molecular markers are non-coding regions of mitochondrial DNA. My question is that why they are used what is the ...
2
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1answer
54 views

Protein-protein interactions search

I used STRING db in order to find all the interactions of the precursor protein APP. What I specifically need is a confirmation (supported by some article and experiments in it). But significant ...
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1answer
107 views

In molecular docking, what is the difference between ligand and cofactor? [closed]

In molecular docking aspect, what is the difference between the Ligand and Cofactor? Can a Cofactor be used like a ligand for docking with the target?
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1answer
66 views

Can exhaustive algorithms produce MSAs that are suitable for 3D structure modelling?

While predicting 3D structure of a protein through homology modelling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
3
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1answer
77 views

Prediction of transmembrane beta barrels?

I studied that prediction of transmembrane alpha helices is more easy and accurate and also good algorithms are available for their prediction. But when we move towards prediction of transmembrane ...
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1answer
23 views

Where can I find SSR and/or SNPs that locate RC1 genes in Soybean? [closed]

Where should I look to find SSR and/or SNPs that locate RC1 genes in Soybean?
4
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1answer
174 views

Why is ab initio protein secondary structure prediction less reliable than alternatives?

To predict secondary structure of proteins three types of Algorithms are used Ab initio, homology based and neural networks. Among these neural networks prove to be more accurate and give good results ...
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1answer
34 views

Obtaining a mapping of RefSeq ACs to Uniprot ACs

I am trying to obtain a mapping for RefSeq Accession Numbers to Uniprot Accession Numbers. I can write a script to do this for a list of RefSeq ACs like this: ...
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0answers
18 views

Looking for hard cell segmentation problem

I am a physicist working on a new image segmentation technique, and I would like to test it by segmenting some images with low-refined cells on a noisy background... Do you know where I could find ...
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0answers
11 views

Oligomeric states of Phyre model

Is it possible to generate an oligomeric state for a phyre model? As it lacks crystal packing information "Generate>Symmetry_mates" obviously does not work in PyMol. I assume that the fit is not ...
4
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1answer
55 views

What does “~mitochondrial DNA ~bp linear DNA” means?

I'm surfing NCBI website -Nucleotide- to find some examples of real DNA sequences to use in my small homework project. My question is related to the title of a DNA sequence below: Sus scrofa ...