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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9
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1answer
133 views

How can I find the mRNA sequence for a specific prokaryotic gene?

What I want to find out is the start of the transcription for a specific gene, how long the UTR is before the actual coding sequence starts. I've looked at various databases like NCBI Gene, Refseq or ...
3
votes
1answer
67 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: ...
4
votes
2answers
65 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, ...
2
votes
1answer
384 views

Plastid and mitochondria

I am not a biologist, so please bear with me for this basic question. Although I tried googling, I am confused. What is the difference between plastids, chloroplasts and mitochondria? Are there any ...
1
vote
0answers
18 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 ...
1
vote
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 ...
0
votes
4answers
272 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 - ...
0
votes
0answers
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 ...
7
votes
1answer
2k views

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 ...
0
votes
2answers
60 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
votes
1answer
49 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
votes
1answer
47 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 ...
0
votes
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 ...
1
vote
1answer
79 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?
0
votes
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: ...
1
vote
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 ...
2
votes
1answer
54 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 ...
1
vote
0answers
71 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
votes
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 ...
1
vote
0answers
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 ...
1
vote
0answers
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 ...
3
votes
1answer
31 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
votes
2answers
118 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
votes
1answer
57 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 ...
1
vote
2answers
65 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
votes
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
votes
1answer
117 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
votes
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 ...
1
vote
0answers
49 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 ...
1
vote
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?
3
votes
3answers
656 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 ...
4
votes
3answers
41 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 ...
1
vote
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
votes
2answers
111 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
votes
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 ...
4
votes
1answer
177 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
votes
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
vote
1answer
115 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
vote
1answer
76 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
votes
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?
14
votes
5answers
1k views

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
votes
1answer
104 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
votes
1answer
65 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
votes
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 ...
0
votes
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 ...
3
votes
2answers
137 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: ...
1
vote
2answers
61 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
votes
1answer
58 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 ...
0
votes
0answers
24 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
votes
1answer
75 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) ...