BOL: Related items

Genomics and Personalized Medicine Breakthroughs

Sun, 01 Jun 2014 23:40:14 -0500

http://bit.ly/e8QGzY Human genome mapping is now enabling a breakthrough in medical innovation -- personalized medicine. What does this mean for patients? We can now identify predispositions to disease, predict how we metabolize drugs, and figure out what kinds of treatments we may respond to, and even determine when a drug may give us an adverse reaction. All medical specialties benefit from human genome intelligence -- oncology saw the first impacts -- but advances are now being seen in cardiology, obstetrics and gynecology, pediatric diseases, gastroenterology, rheumatology, immunology and other areas. This video covers the areas that genetic medicine is impacting and where the future of genomic medicine is heading.

TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads

Surabhi Chaudhary — Tue, 15 May 2018 02:53:11 -0500

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

How to use TAREAN:

Install a local instance of the pipeline using its source code available from bitbucket repository.
Use public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

Genomic Medicine - Bruce Korf (2014)

Tue, 24 Jun 2014 07:58:44 -0500

May 21, 2014 - Current Topics in Genome Analysis 2014 A lecture series covering contemporary areas in genomics and bioinformatics. More: http://www.genome.gov/COURSE2014

Integrative Genomics Viewer (IGV) tutorial

Neel — Sat, 12 Jul 2014 15:16:23 -0500

The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.

http://www.broadinstitute.org/igv/

Address of the bookmark: https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial

COSMOS, our workflow management system for NGS data

Jit — Wed, 23 Jul 2014 07:29:14 -0500

COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via Advance Access in Bioinformatics (Gafni et al. 2014). It is also available for download for non-commercial academic and research purposes at:

http://cosmos.hms.harvard.edu/.

Address of the bookmark: https://cosmos.hms.harvard.edu/

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.

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

Jit — Wed, 06 Dec 2017 02:08:14 -0600

An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/cope

Tools for bacterial whole genome annotation

Radha Agarkar — Sat, 16 Dec 2017 17:37:47 -0600

RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation (if you have only a few genomes to annotate).

Prokka – Standalone command line tool, takes just a few minutes per genome. This is the best way to get good quality annotation in a flash, which is particularly useful if you have loads of genomes or need to annotate a pangenome or metagenome. Note however that the quality of functional information is not as good as RAST, and you will need several extra steps if you want to do functional profiling and pathway analysis of your genome(s)… which is in-built in RAST.

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

PGAP: NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

BEACON (automated tool for Bacterial GEnome Annotation ComparisON), a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.

BlastKOLA: Assigns K numbers to the user's sequence data by BLAST searches, respectively, against a nonredundant set of KEGG GENES. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to this server and can be executed in an interactive mode. BlastKOALA is suitable for annotating fully sequenced genomes.

PAGIT: Provides a toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four tools: (i) ABACAS which classifies and orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying and correcting small errors in consensus sequences and; (iv) RATT for help annotation. The software was mainly created to analyze parasite genomes of up to about 300 Mb.

MAKER: A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).

MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.

Circlator: automated circularization of genome assemblies using long sequencing reads

Poonam Mahapatra — Tue, 15 May 2018 09:42:32 -0500

A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481.

Address of the bookmark: http://sanger-pathogens.github.io/circlator/

mScaffolder: A comparative genome scaffolding tool

Jit — Fri, 15 Jun 2018 04:48:01 -0500

A comparative genome scaffolding tool based on MUMmer

mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to the reference genome. Please send your questions and comments to mchakrab@uci.edu.

Citation https://www.nature.com/articles/s41588-017-0010-y

Address of the bookmark: https://github.com/mahulchak/mscaffolder