BOL: Related items

Edit DNA !!!

Jit — Wed, 05 Mar 2014 02:27:54 -0600

A genome-engineering tool known as Crispr may allow scientists to alter the DNA of humans, animals and plants, a research breakthrough that promises to make a significant impact on science and fighting diseases, according to a March 3 story in the New York Times. Scientists hope Crispr might also be used for genomic surgery, as it were, to correct errant genes that cause disease.

A rescently publication paper ( http://jb.asm.org/content/169/12/5429.long )shows significance of an unusual repeated DNA sequences next to a gene in a common bacterium, and their scientific significance. The sequences, it turns out, are part of a sophisticated immune system that bacteria use to fight viruses. And that system, whose very existence was unknown until about seven years ago, may provide scientists with unprecedented power to rewrite the code of life. This means a genome can be edited, much as a writer might change words or fix spelling errors. It allows “customizing the genome of any cell or any species at will,”.

Reference:

http://www.prweb.com/releases/2014/03/prweb11636031.htm

http://www.nytimes.com/2014/03/04/health/a-powerful-new-way-to-edit-dna.html?hpw&rref=health

http://jb.asm.org/content/169/12/5429.long

Scripted DNA !!!

Jit — Mon, 17 Aug 2015 17:44:04 -0500

As per bioinformatician DNA is partially scripted ;) You dont believe in it. Please have a look at image carefully:)

FSA: Fast Statistical Alignment

Jit — Mon, 06 Feb 2017 04:26:01 -0600

FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise comparisons, developed by Ariel Schwartz in "Posterior Decoding Methods for Optimization and Control of Multiple Alignments."

FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments:

FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This "query-specific learning" alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints.
FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy.
FSA can quickly align very long sequences using the "anchor annealing" technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above.
The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned (see the picture and movie at the top of the page).

You can see more information on the FAQ.

Address of the bookmark: http://fsa.sourceforge.net/

Tetra-Nucleotide Analysis

Jit — Thu, 04 May 2017 05:07:41 -0500

A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial genomes contain useful, albeit weak, phylogenetic signals. Even though tetra-nucleotide analysis (TNA) utilizes the information of whole genome, it is evident that it cannot replace other alignment-based phylogenetic methods such as OrthoANI or 16S rRNA phylogeny. However, TNA can be useful for phylogenetic characterization when whole genome or 16S rRNA gene information is not available. For example, a partial genomic fragment obtained from a metagenome can be identified by TNA (Teeling et al., 2004). TNA is also fast enough that it can be used as a search engine against a large genome database.

Address of the bookmark: https://chunlab.wordpress.com/tetra-nucleotide-analysis/

SLIDESORT-BPR

Abhimanyu Singh — Mon, 20 Nov 2017 09:19:52 -0600

Chromosomal rearrangement events are caused by abnormal breaking and rejoining of DNA molecules. They are responsible for many of the cancer related diseases. Detecting the DNA breaking and repairing mechanism, therefore, may offer vital clues about the pathologic causes and diagnostic/therapeutic target of these diseases. But this effort also poses considerable challenges, because the structural variations and the genomes are different from one person to another. Intermediate comparison via reference genome could lead to the loss information. Unlike the current methods which make use the reference genome, we developed a method to detect the breakpoint reads directly from observing the differences between two (or more) NGS short reads samples. Slidesort-BPR is a command line tool implemented in C++.

Address of the bookmark: https://github.com/ewijaya/slidesort-bpr

Ra assembler - a de novo DNA assembler for third generation sequencing data

biogeek — Wed, 27 Dec 2017 20:36:54 -0600

Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).

Ra is in development since 2014 in the form of several separate components that used to be run individually.
This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.

Unlike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphmap) and constructing and reducing an overlap graph (Ra layout, https://github.com/mariokostelac/ra).

Address of the bookmark: https://github.com/mariokostelac/ra-integrate/

Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment

Poonam Mahapatra — Sat, 02 Jun 2018 07:36:05 -0500

Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its use as simple as possible without loosing the functionality that it is necessary in most of the cases. Other options can be changed in the stand-alone program. You can see here an example output file showing the blocks selected from a protein alignment. Further information can be found in the online documentation.

Address of the bookmark: http://molevol.cmima.csic.es/castresana/Gblocks_server.html

3D de novo assembly (3D DNA) pipeline

Jit — Sun, 02 Feb 2020 13:41:55 -0600

For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly.

For the original version of the pipeline and to reproduce the Hs2-HiC and the AaegL4 genomes reported in (Dudchenko et al., Science, 2017) see the original commit.

For the detailed description of the merge section see https://github.com/theaidenlab/AGWG-merge.

Address of the bookmark: https://github.com/theaidenlab/3d-dna

ExRec: Exclusion of Recombined DNA

LEGE — Wed, 27 Mar 2024 20:48:26 -0500

ExRec (Exclusion of Recombined DNA) is a Python pipeline that implements the four-gamete test to filter out recombined DNA sites from up to thousands of DNA sequence loci. The pipeline consists of five standalone applications: the first two convert folders of NEXUS or PHYLIP files into the standard input file for the main program that conducts the four-gamete filtering procedures. The pipeline outputs recombination-filtered data in concatenated NEXUS and PHYLIP formats and a tab-delimited table containing descriptive statistics for all loci and the results. This software also allows the user to output the longest non-recombined sequence blocks from loci (current best practice) or randomly select non-recombined blocks from loci (a newer approach). Two other applications in the package convert the recombination-filtered data into single-locus NEXUS or PHYLIP files. The ExRec package can thus facilitate species delimitation, species tree, and historical demography studies by providing loci that better meet the no-recombination assumption in coalescent-based analyses.

Link to the article: https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad174/7455250?searchresult=1

Link to the software:
https://github.com/Sammccarthypotter/ExRec

Address of the bookmark: https://github.com/Sammccarthypotter/ExRec

List of motif discovery tools !

Neel — Tue, 20 Nov 2018 03:54:26 -0600

In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino acids which may not be adjacent.

Following are the list of tools for motif discovery:

2Dsweep -- protein annotation by secondary structure elements

Perform secondary structure predictions on protein sequences.

3D-footprint -- database of DNA-binding protein structures

Find binding specificity information about DNA-protein complexes.

3D-footprint: DNA-binding protein database

Find information about the binding specificity of DNA-binding proteins.

3D-partner -- a web server to infer interacting partners and binding models

Predict interacting partners and binding models.

3MOTIF -- a protein structure visualization system for conserved sequence motifs

Use this web-based sequence motif visualization system to display sequence motif information in its appropriate three-dimensional (3D) context.

AFAWE -- Automatic functional annotation in a distributed Web Services Environment

Protein function prediction and annotation in an integrated environment powered by web service.

ANCHOR -- Prediction of Protein Binding Regions in Disordered Proteins

Find information about protein binding.

ANNIE -- ANNotation and Interpretation Environment for Protein Sequences

Use to predict function from de novo protein sequences.

Active Sequences Collection (ASC) database -- A new tool to assign functions to protein sequences

Search for short active protein sequences with demonstrated biological activities.

Blocks -- Ungapped segments in conserved protein sequences

Search for ungapped segments corresponding to the most highly conserved regions of proteins.

CASTp -- computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

Identify and measure surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.

CSA -- The Catalytic Site Atlas

To search for catalytic residue annotation for enzymes in the Protein Data Bank.

ConFunc -- Conserved residue Protein Function Prediction Server

Predict protein function using Gene Ontology.

ConSurf-DB -- evolutionary conservation profiles of protein structures database

Automatically calculate evolutionary conservation scores of key amino acid residues and map them on protein structures.

DBAli -- A Database of Structure Alignments

Mine the protein structure space.

DILIMOT -- discovery of linear motifs in proteins

Predict short linear motifs (3-8 residues) in a set of protein sequences.

Dasty2 -- an Ajax protein DAS client

A web client for visualizing protein sequence feature information using DAS.

DomainSweep -- protein annotation by domain analysis

Identify the domain architecture within a protein sequence.

E1DS -- catalytic site prediction based on 1D signatures of concurrent conservation

Predict enzyme catalytic site.

ELM -- Eukarotic Linear Motif Resource

Predict functional sites in eukaryotic proteins.

EXPASY Proteome Tools Collection

Use a collection of tools for protein analyses.

EXPASY-Findmod

Predict potential protein post-translational modifications and find potential single amino acid substitutions in peptides.

EzCatDB -- the Enzyme Catalytic-mechanism Database

Search for information related to the catalytic mechanisms of enzymes.

FFPred -- feature-based function prediction

An integrated feature-based function prediction server for vertebrate proteomes.

FingerPRINT Scan

Identify the closest matching PRINTS sequence motif fingerprints in a protein sequence.

FireDB -- a database of functionally important residues from proteins of known structure

Search for functional annotation of important sites in proteins with known structures.

Frog2 -- a FRee Online druG 3D conformation generator

Produce 3D conformations of small drug compounds.

HGPD -- Human Gene and Protein Database

A database presenting experiment-based results in human proteomics.

HHsenser -- exhaustive transitive profile search using HMMx96HMM comparison

Conduct exhaustive intermediate profile searches of a set of homologous protein sequences.

HotSpot Wizard -- Substrate Specificity Hot Spot Identification web server

Design protein mutations in site-directed mutagenesis.

INTREPID -- INformation-theoretic TREe traversal for Protein functional site IDentification

Use for protein functional site identification.

Integrating protein annotation resources through the Distributed Annotation System

Annotate protein using this integrated annotation resource.

InterProScan -- protein domains identifier

Identify protein family (and DNA) domains, patterns, motifs, protein families, and functional sites.

KFC -- Knowledge-based FADE and Contacts

Interactive forecasting of protein interaction hot spots.

MAGIIC-PRO -- detecting functional signatures by efficient discovery of long patterns in protein sequences

Discover long patterns in protein sequences.

MALISAM -- Manual ALIgnments for Structurally Analogous Motifs

Database containing pairs of structural analogs and their alignments.

MEME -- discovering and analyzing DNA and protein sequence motifs

Find sequence patterns in DNA and protein sequences.

MODPROPEP -- a program for knowledge-based modeling of protein-peptide complexes

A web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases.

MeMo -- a web tool for prediction of protein methylation modifications

Predict protein methylation sites.

MegaMotifBase -- a database of structural motifs in protein families and superfamilies

Find structural segments or motifs for protein structures.

Minimotif Miner -- a tool for investigating protein function

Find motifs in a protein sequence.

Motif3D -- Relating protein sequence motifs to 3D structure

Visualize protein sequence motifs on the 3D protein structures.

MotifScan

Find presence of any known protein motif (Prosite and Pfam) in a protein sequence.

MultiBind -- Multiple Alignment of Protein Binding Sites

Recognize spatial chemical binding patterns common to a set of protein structures.

NMT -- The MYR Predictor

Analyze proteins for the presence of N-terminal N-myristoylation site.

NetNGlyc -- N-Glycosylation sites prediction tool

Find the presence of N-Glycosylation sites in human proteins.

NetOGly 3.1 -- O-glycosylation sites prediction tool

Find the presence of O-GalNAc (mucin type) glycosylation sites in mammalian proteins.

NetPhos 2.0 -- Phosphorylation sites predictions

Analyze eukaryotic proteins for the presence of serine, threonine and tyrosine phosphorylation sites.

NetPhosK 1.0 Server -- kinase specific eukaryotic protein phosphorylation sites prediction tool

Find possible kinase specific phosphorylation sites in eukaryotic proteins.

NetworKIN -- a resource for exploring cellular phosphorylation networks

NeuroPred -- a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides

Predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences.

Non-Redundant Patent Sequences - Patented Sequence Database

Find information about patented nucleotide and protein sequences.

O-GLYCBASE

Search for information about glycoproteins with O-linked and C-linked glycosylation sites.

PANDORA -- Protein ANnotation Diagram ORiented Analysis

Find information about protein sequence annotations.

PAR-3D -- Protein Active site Residue - 3D structural motif

A server to predict protein active site residues.

PDBSite -- a database of the 3D structure of protein functional sites

Search for structural and functional information on the protein functional sites.

PDBSiteScan -- A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins

Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites.

PEDANT -- Protein Extraction, Description and ANalysis Tool

Conduct genome wide functional and structural analysis.

PHOSIDA -- Phosphorylation site database

Search for phosphorylation data of any protein of interest.

PHOSPHORYLATION SITE DATABASE

Search for information on prokaryotic proteins that undergo serine, threonine, or tyrosine phosphorylation.

PNU -- Protein Naming Utility

Determine correct names for proteins.

POODLE-S -- Predicition Of Order and Disorder by machine LEarning

Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.

PPISearch -- Protein-Protein Interaction Search

Find homologous protein-protein interactions across multiple species.

PPSearch

Search your query sequence against PROSITE pattern database for protein motifs.

PRIDB -- Protein-RNA Interface DataBase

Find information about protein-RNA complexes from the Protein Data Bank (PDB).

PRINTS and its automatic supplement, prePRINTS -- A compendium of protein fingerprints

Search for protein fingerprints.

PROSITE

Identify protein families and domains for a given protein sequence.

PRRDB -- Pattern Recognition Receptor Database

A comprehensive database of pattern-recognition receptors and their ligands.

PatMatch -- a program for finding patterns in peptide and nucleotide sequences

Search for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences.

PepCyber:P~PEP -- a database of human protein protein interactions mediated by phosphoprotein-binding domains

Database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions.

PeptideCutter -- protein cleavage sites prediction tool

Predicts potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence.

Phobius -- A combined transmembrane topology and signal peptide predictor

Predict combined transmembrane topology and signal peptides.

Phospho.ELM -- a database of phosphorylation sites

Search for eukaryotic phosphorylation sites.

Phospho3D -- a database of three-dimensional structures of protein phosphorylation sites

Search for 3D structure and functional annotation of phosphorylation sites in proteins.

PhosphoSite -- A bioinformatics resource dedicated to physiological protein phosphorylation.

Search the database of in vivo phosphorylation sites of human and mouse proteins

PolyQ -- Polyglutamine Database

Find information about polyglutamine (polyQ) repeats.

Pratt Protein motif and pattern discovery

Find the presence of protein motifs and patterns in an amino acid sequence.

PrediSi -- Prediction of Signal Peptides and their Cleavage Positions

Predict signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences.

ProFunc -- a server for predicting protein function from 3D structure

Predict protein functions based on known structures.

ProMateus--an open research approach to protein-binding sites analysis

Predict the location of potential protein-protein binding sites for unbound proteins.

ProTeus -- identifying signatures in protein termini

Identify short linear signatures in protein termini.

ProtSweep -- protein annotation by homology

Analyze and identify newly obtained protein sequences.

Protemot -- prediction of protein binding sites with automatically extracted geometrical templates

Predict protein binding sites in a protein sequence based on geometrical analysis of protein tertiary substructures.

QuasiMotiFinder -- protein annotation by searching for evolutionarily conserved motif-like patterns

Search for evolutionarily conserved motif-like patterns in protein sequences.

RNABindR -- software for prediction of RNA binding residues in proteins

Web-based server for analyzing and predicting RNA binding sites in proteins.

SCANMOT -- searching for similar sequences using a simultaneous scan of multiple sequence motifs

Search for similarities between proteins by simultaneous matching of multiple motifs.

SDPpred -- A Tool for Prediction of Amino Acid Residues that Determine Differences in Functional Specificity of Homologous Proteins

Predict residues in protein sequences that determine the proteins' functional specificity.

SDR -- Specificity Determining Residues Database

Predict specificity-determining residues in protein families.

SLiMDisc -- Short, Linear Motif Discovery

Find shared motifs in proteins with a common attribute.

SUMOsp -- a web server for sumoylation site prediction

Conduct in silico sumoylation sites prediction.

SWAKK -- a web server for detecting positive selection in proteins using a sliding window substitution rate analysis

Detect protein sequence section under positive evolution selection.

ScanProsite

Search for motifs and patterns within protein sequences.

ScanProsite -- detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

Detect patterns, profiles and motifs in a protein sequence.

ScanSite 2.0 -- Proteome-wide prediction of cell signaling interactions using short sequence motifs

Search for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

SePreSA -- SErver for the PREdiction of populations susceptible to Serious Adverse drug reaction

Find information about populations carrying polymorphisms within protein binding pockets that make them susceptible to serious adverse drug reaction (SADR).

Sequence Motif Search

Search the presence of a motif in either amino acid sequence or nucleotide sequence.

Signal-3L -- A 3-layer approach for predicting signal peptides

Predict signal peptides.

SignalP -- Machine learning approaches to the prediction of signal peptides, their cleavage sites, and other protein sorting signals

Predict signal peptides and their cleavage sites.

Sulfinator -- tyrosine sulfation sites prediction tool

Predict the presence of tyrosine sulfation sites in protein sequences

SuperSite -- Ligand Binding Site Database

Look at protein structure from a ligand and binding site perspective.

Swiss EMBnet node web server

Use a collection of bioinformatics tools at this portal site.

T-REKS -- identification of Tandem REpeats in sequences with a K-meanS based algorithm

Find information about tandem repeats in proteins that carry fundamental biological functions and are related to a number of human diseases.

TMFunction -- The Functional Database of Membrane Proteins

Find information about functional residues in alpha-helical and beta-barrel membrane proteins.

TOPDOM -- Conservatively Located Domains and Motifs in Transmembrane Proteins

Database of domains and motifs with conservative location in transmembrane proteins.

The EMOTIF database

Search for highly conserved and specific protein sequence motifs.

TreeDet -- Predicting Functional Residues in Protein Sequence Alignments

Predict functional sites in protein sequence alignments use different methodologies.

W-ChIPMotifs -- ChIP-based protein Motif discovery web server

Find de novo protein motifs from chromatin immunoprecipitation data.

WebFEATURE -- an interactive web tool for identifying and visualizing functional sites on macromolecular structures

Scan query structures for functional sites in both proteins and nucleic acids.

WebProAnalyst -- an interactive tool for analysis of quantitative structurex96activity relationships in protein families

Analyze quantitative structure-activity relationship of related protein families.

eBLOCKs -- enumerating conserved protein blocks to achieve maximal sensitivity and specificity

Search for ungapped alignments of highly conserved regions among a protein family or superfamily.

eF-seek -- prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape

Predict the functional sites of proteins.

firestar -- prediction of functionally important residues using structural templates and alignment reliability

An expert system for predicting ligand-binding residues in protein structures.

iMOTdb -- a comprehensive collection of spatially interacting motifs in proteins

Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.