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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What is Mendelian Randomization, and how is it used to infer causality in epidemiology?

Studies of human traits and diseases are inherently confined to observational studies, known as epidemiological studies. This can make it very hard to determine what actually causes a particular ...
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2answers
50 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.
3
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1answer
45 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 ...
2
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1answer
46 views

Conserved acetylation sites in a given protein

I want to identify potential conserved Acetylation sites in protein X. As it is known, acetylation happens in Lysines (K), thereby I would like to identify conserved K residues for protein X during ...
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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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1answer
55 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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32 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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1answer
53 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 ...
2
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1answer
50 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
61 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 ...
0
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1answer
42 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 ...
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0answers
14 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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0answers
20 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 ...
3
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1answer
28 views

Gemini usage of --sample-filter

I am using gemini to query databases made from vcf files, which contain data from multiple samples. However, I need to query data only from one sample, (for which I currently use grep to filter the ...
4
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2answers
101 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 ...
3
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1answer
43 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
52 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 ...
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 ...
4
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1answer
58 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. ...
0
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1answer
25 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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0answers
46 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 ...
0
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1answer
58 views

Predicting 3D structure of a protein?

While predicting 3D structure of a protein through homology modeling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
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0answers
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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3answers
613 views

Bioinformatics tool for “pairwise alignment” of complementary sequences?

I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate ...
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0answers
29 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 ...
4
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3answers
35 views

Identifiying a conserved residue in multiple PDB structures

I have a few hundred PDB structures of the same protein, and I need to identify a specific conserved residue in all of them. Originally I wanted to extract the sequences from the PDB files with ...
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1answer
35 views

BWA-MEM single strand or doublestrand alignment

In whole genome secondary analysis does BWA-MEM use a double stranded fasta reference or are reads aligned to only one, single stranded fasta reference?
4
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2answers
78 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
30 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 ...
4
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1answer
163 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 ...
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 ...
1
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1answer
73 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?
1
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1answer
71 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 ...
0
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1answer
20 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?
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5answers
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Why did high A+T content create problems for the Plasmodium falciparum genome project?

The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
5
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1answer
92 views

Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
0
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1answer
56 views

results of FgenesH and GenScan

Why FgenesH and Genscan don't give good results as I have prdicted number of genes of Chromosome 16 which according to NCBI are 86 but the results I have obtained are 57 genes predicted by FgenesH and ...
0
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0answers
16 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
7 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 ...
3
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2answers
118 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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2answers
51 views

How is e-value calculated in BLAST 2 sequences (BLAST+)?

In the BLAST+ packages, you can align two sequences instead of searching a database: tblastn -query seq1.fa -subject seq1.fa The web BLAST documentation states ...
4
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1answer
47 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 ...
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0answers
20 views

NMDS analysis - weird plots

I ran a NMDS analysis on 16S tag sequencing data on three different 16S regions, and would like to establish the regression coefficients (R, p) from this. All the data is stored within a combination ...
4
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1answer
61 views

Question about SAM CIGAR string

My question is about the CIGAR specification. The documentation states: M 0 alignment match (can be a sequence match or mismatch) ...
1
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2answers
47 views

identifying which SNPs sit in TFBS (Yeast)

i have a set of ~11k SNPs for Saccharomyces cerevisiae, baker's yeast and i would like to identify which ones of these sit in transcription factor binding sites and if they do information on the ...
1
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1answer
56 views

From STRUCTURE to FSTAT format

From numerical simulations I output a file that is input to STRUCTURE (Hubisz et al. 2009). I now realize that I would need to process my data with FSTAT (Goudet 1995). Both are text files. Is there ...
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0answers
11 views

Where to Find Pedigree-Linkage Data for Computational Pedigree Analysis

I'm currently working on a project that uses graphical models (Bayesian networks) for pedigree analysis. My group developed a few models several months ago, but the original data used to develop the ...
0
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0answers
45 views

Interpreting soft clipping in a SAM alignment

I am interpreting CAGE data. I have noticed that in the SAM files I am analysing, there are many pairs of lines of the form (e.g.) ...
1
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1answer
80 views

What are the basic skills required to pursue future studies in theoretical ecology? [closed]

I am a student and just about to choose a project for my Master's thesis in biology. I want to pursue studies in theoretical ecology in the future. Between field ecology and computational biology (as ...
0
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1answer
18 views

what is the principle behind Allele Frequency Net Database

I just wanted to know what is the basic principle of Allele*Frequency Net Database. How are the frequencies present in them calculated??