BOL: Related items

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.

Bioinformatics Articles links

Jitendra Narayan — Sat, 10 Aug 2013 07:44:34 -0500

I found several useful bioinformatics articles which exaplain, define and elaborate the bioinformatics in scientific way. Therefore, instead of writting it again I decided to share it with you. Here is the list of some useful bioinformatics articles:

What is Bioinformatics - An introduction article by Mark Gerstein at Yale University.
The powerful world of bioinformatics
Bioinformatics: Key to 21st Century Biology
The commercialization of bioinformatics by Phillip B.C. Jones
A Curriculum for Bioinformatics: The Time is Ripe This article proproses requirements for a standard bioinformatics curriculum. By Russ Altman.
Human Genome Research A description of the Human Genome Project.
Retooling for Bioinformatics An article from The Scientist
A Programming Course in Bioinformatics A discussion of the task of teaching an introductory bioinformatics course. By Russ Altman and John Koza.
Sequence analysis Keith Robison's guide to the exciting world of biosequence comparison! Useful background information on a variety of computational biology algorithms.
Bioinformatics, Supercomputing, and Complex Genome Analysis ,DOE/NIH Human Genome News , 4(5) January 1993.
Medical Informatics Training at Stanford University School of MedicineAn article from 1995 by Edward Shortliffe describing our medical informatics training program, the nature of the curriculum, the backgrounds of our students, and the career paths of our graduates.
Elementary Sequence Analysis - Database Searching by B. Golding Jan 1996. Fasta, blast, blitz, blaze, flash, blocks.
Bioinformatics in Support of Molecular Medicine A description of bioinformatics and its connection to clinical informatics. By Russ Altman.
Biology as a Business Venture and the Rise of Bioinformatics , 1996.
Preface to Molecular Bioinformatics- Sequence Analysis , 1997.
Bioinformatics & Cheminformatics in the Drug Discovery Cycle , 1997.
Bioinformatics in a post-genomics age Sept 1997
Bioinformatics takes charge , Trends in Biotech. , Vol. 16 No. 3 (170), pp. 104-107, March 1998.
"A Curriculum For Bioinformatics: The Time Is Ripe" An editorial from the journal BIOINFORMATICS-Bioinformatics, Vol 14, Issue 7, pages 549-550 (August 1998)
Bioinformatics, pharma and farmers , Trends in Biotech. , Vol. 17 No. 3 (182) , pp. 85-88. March 1999.
Bioinformatics/Computational Biology Programs (May 1999)
Biocomputing For Everone an introduction to biocomputing for the layperson published by the VSNS biocomputing division.
Biocomputing For Schools Another VSNS publication - this time aimed at highschool students, but fun to read for everyone. Includes articles on the application of bioinformatics to BSE research, and a ``Do-It-Yourself'' detailed example of a WWW search.
Understanding the human genome By D. L. Brutlag, in Scientific American: Introduction to Molecular Medicine , P. In Leder, D. A. Clayton, E. Rubenstein, Eds., (New York: Scientific American , 1994), pp. 153-168.
Viva bioinformatics, but who survives? , 1999.
Bioinformatics: Playing The Numbers Game June 1999
Mining the Genome Sept 1999
Commercialization of biological information and the rise of bioinformatics - Part I , Nov/Dec 1999, 20/21, pp. 40-47.
Commercialization of biological information and the rise of bioinformatics - Part II , Jan 2000, pp. 51-56.
Turbo-charging bioinformation for drug discovery , Feb 2000, pp. 38-49.
Bioinformatics: low supply, high demand June 2000
The Next Wave of the Genomics Business July 2000
The Bioinformatics Gold Rush July 2000
Bioinformatics . Next Wave feature on careers in bioinformatics.September 2000
A prerequisite for working in thie field: love of computers article from The Scientist (Nov 2000)
Sep/Oct 2000 issue of the MIT Technology Review
How to become a bioinformatics expert , including a listing ofEuropean opportunities to study bioinformatics. Compiled by theVirtual School of Natural Sciences BioComputing Division.
Protein Sequence Alignment and Database Scanning Geoff Barton's review.
Pattern matching and motifs
Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines
VHG Virtural HyperGlossary. Defines terms used in different subfields, currently Glycoscience, Protein Structure.
LASSAP a LArge Scale Sequence compArison Package
Bioinformatics in pre- and post-genomics eras , Trends in Biotech. ,Vol. 18 , pp. 133-135, April 2000.
Confluence of Western and Traditional Medicines and Future Prospectes - Part I , Mar/Apr 2000, pp. 34-37.
Confluence of Western and Traditional Medicines and Future Prospectes - Part II , May/Jun 2000, pp. 66-74.
Computers + Biology = Bioinformatics April 2001
Bioinformatics U., Genome Technology, September, 2001 An article from Genome Technology written by Nat Goodman about bioinformatics curricula.
Training in a Hybrid Discipline, Nature, October 25, 2001 An article from Nature written by Potter Wickare and Paul Smaglik on bioinformatics training programmes in North America.
Bioinformatics Knowledge Vital to Careers - Competition from mathematicians and computer scientists compels biologists to become computational article from The Scientist (Sept 2002)
The babel of bioinformatics By Teresa Attwood, Science , 5491: 471 (2000).
The quiet revolution: Biodiversity informatics and the internet By Frank A. Bisby, Science , 289: 2309 (2000).
Are you ready for the revolution? By Declan Butler, Nature , 409: 758-760 (2001).
Beyond the genome: Biotech's next holy grail By Ellen Licking, Business Week , April 10, 2000.
The genome explained By Ellen Licking, Business Week , June 12, 2000.
Why bioinformatics is hot career By Stacey Wells, San Francisco Chronicle , March 4, 2001.
Proteomics: Beyond the genome Edited by Patricia O'Connell, Business Week Online, June 7, 2001.
A true believer dismisses indifference to bioinformatics By Terence Chea, Washington Post , March 14, 2002.
Genome map on a grain of rice By Kristen Philipkoski, Wired News , March 29, 2002.
Informatics moves to the head of the class By Beth Schachter, Bio-IT World , June 12, 2002.
The proteomics odyssey By Malorye Branca, Bio-IT World , Aug. 13, 2002.
Dell goes nuts for clusters By Michael Kanellos, CNET News.com , Sept. 2, 2002.
IBM teams with TurboGenomics By Salvatore Salamone, Bio-IT World , Sept. 5, 2002.
The new, new pharmacogenomics By Malorye Branca, Bio-IT World , Sept. 9, 2002.
RLX introduces a biocluster in a box By Salvatore Salamone, Bio-IT World , Sept. 17, 2002.
CombinatorX gets $40 million to look for drug synergies By Salvatore Salamone, Bio-IT World , Sept. 24, 2002.
Calculating with DNA By Salvatore Salamone, Bio-IT World , October 2002.
Hitachi Soft develops low-cost human genome DNA chip By Kuriko Miyake, ITworld.com , Oct. 8, 2002.
IBM chooses Linux for 'Blue Gene' supercomputer By Lisa Gill,NewsFactor Network , Oct. 24, 2002.
The international 'HapMap' project cbsnews.com , Oct. 29, 2002.
US stem cell policy deters investors By Steve Mitchell, UPI , Nov. 2, 2002.
Biochip sprouts DNA strands By Kimberly Patch, Technology Research News , Nov. 13, 2002
Genomics consolidation ï¿½ no pain, no gain By Malorye Branca, Bio-IT World , Dec. 10, 2002.
Data stored in multiplying bacteria By Natasha McDowell,NewScientist.com , Jan. 3, 2003.
Cowabunga! Scientists to start Bovine Genome Project Science Daily , March 5, 2003.
Computational Analysis of Complexity in Gene Expression Arrays
Building your own Bioinformatics Supercomputer for Cheap Using Grid Technology
Career Advice for Computational Biology By Amjad-Ali Khoja at U. Texas.
Proceedings of the National Academy of Sciences
A Practical Guide to protein sequence and structure analysis at UCL

Feel free to add more useful article links below by commenting on this page. Your comments are welcome.

LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

LEGE — Fri, 17 Sep 2021 01:57:02 -0500

The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed lncRNAs annotation strategy, optimized calculating efficiency, diversified classification and interactive analysis report. LncPipe allows users additional control in interuppting the pipeline, resetting parameters from command line, modifying main script directly and resume analysis from previous checkpoint.

Ref https://www.lncrnablog.com/lncpipe-a-nextflow-based-pipeline-for-identification-and-analysis-of-long-non-coding-rnas-from-rna-seq-data/

Address of the bookmark: https://github.com/likelet/LncPipe

NCBI Datasets pages

BioStar — Wed, 12 Jul 2023 06:29:31 -0500

Update! Assembly and Genome record pages now redirect to new NCBI Datasets pages. NCBI Datasets is a new resource that makes it easier to find and download genome data. Learn more: https://ncbiinsights.ncbi.nlm.nih.gov/2023/07/11/ncbi-datasets-genome-assembly-pages/ #NCBICGR

Effective July 10, 2023, NCBI’s Assembly and Genome record pages now redirect to new NCBI Datasets pages. As previously announced, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.  

The following pages have been updated:

The NCBI Assembly record pages now redirect to the new NCBI Datasets Genome record pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST. 
The NCBI Genome record pages now redirect to the NCBI Datasets Taxonomy record pages that provide a taxonomy-focused portal to genes, genomes, and additional NCBI resources.

During this transition, you will have the option to return to the legacy Genome and Assembly record pages. We will remove the legacy pages in early 2024. 

Want to Know which genome assembler rule the world ?

Rahul Agarwal — Sun, 11 Aug 2013 11:42:32 -0500

Assemblathon 2: evaluating de novo methods of genome assembly

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

The Story of You: ENCODE and the human genome

Sat, 24 Aug 2013 18:49:03 -0500

Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE

DNA is packaged in a chromosome experiment

Mon, 23 Sep 2013 18:01:12 -0500

For more information, log on to- http://shomusbiology.weebly.com/ Download the study materials here- http://shomusbiology.weebly.com/bio-materials.html A nucleosome is the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around four histone protein cores.[1] This structure is often compared to thread wrapped around a spool.[2] Nucleosomes form the fundamental repeating units of eukaryotic chromatin,[3] which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter). Nucleosomes are folded through a series of successively higher order structures to eventually form a chromosome; this both compacts DNA and creates an added layer of regulatory control, which ensures correct gene expression. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosomes were observed as particles in the electron microscope by Don and Ada Olins [4] and their existence and structure (as histone octamers surrounded by approximately 200 base pairs of DNA) were proposed by Roger Kornberg.[5][6] The role of the nucleosome as a general gene repressor was demonstrated by Lorch et al. in vitro [7] and by Han and Grunstein in vivo.

How I discovered DNA - James Watson

Fri, 18 Oct 2013 11:30:26 -0500

View full lesson: http://ed.ted.com/lessons/james-watson-on-how-he-discovered-dna Nobel laureate James Watson opens TED2005 with the frank and funny story of how he and his research partner, Francis Crick, discovered the structure of DNA. Talk by James Watson.

Dynamic chromosome breakpoints !!!

Jitendra Narayan — Wed, 13 Aug 2014 18:38:10 -0500

Cell division involves the distribution of identical genetic material, DNA, to two daughters’ cells. During this process, duplicated deoxyribonucleic acid (DNA) goes through a condensation and decondensation process. This is followed by nuclear envelope dissolution, mitotic spindle assembly, migration of the sister chromatid pairs to the metaphase plate, division and segregation of identical sets of chromosomes into daughter nuclei and nuclear envelope reformation.

The vital metaphase stage of cell division, when the sister chromatids migrated to the centre and lined up in a row, and pulled apart using attached microtubules in such a way that half the DNA ends up in each daughter cell. However, before the mitotic spindle‐mediated movement gets start and pulled DNA apart, the chromosomes are free to undergo recombination which involves the exchange of genetic material either between multiple chromosomes or between different regions of the same chromosome.

During recombination, the precise breakage of each strand, exchange between the strands, and sealing of the resulting recombined molecules happens. The “chromosomal breakpoints” refers to these places where they break. Mostly, this process occurs with a high degree of accuracy at high frequency in both eukaryotic and prokaryotic cells. But occasionally this “break and sealing/ break and reattach” process goes wrong and the reattachment happens in the wrong place which usually create disaster (with few exceptions).These chromosome disaster or abnormalities involve the gain, loss or rearrangement of visible amounts of genetic material during cell division. These abnormalities are of two type, the first one is numerical abnormalities where severe disorders are caused by the loss or gain of whole chromosomes, which affect the copy number of hundreds or even thousands of genes. The second are structural abnormalities which can be unbalanced or balanced. The former are similar to numerical abnormalities in that genetic material is either gained or lost. The natural defects in chromosome segregation are linked to cancer and several genetic diseases (http://en.wikipedia.org/wiki/List_of_genetic_disorders). Therefore, the enzymes involved in regulating cell division are still the attractive drug targets for many diseases.

Apart from certain chromosome abnormalities, these “crossing over” of segments of maternal and paternal chromosomes to form hybrid chromosomes have some evolutionary importance and considered as a driver of genetic variation. Moreover, the chromosome breakage in evolution is considered to be non-random in nature(http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020014). In addition the study of breakpoint regions and non-breakpoint (stable) regions of chromosomes indicates both the regions evolved in distinctly different ways ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/). These breakage may lead to genetic diseases or participate to chromosomal rearranmgnets and contributed in development of new species.

I will try to explain the genome hotspots/Evolutionary Breakpoint Regions(EBRs)/fragile regions/weak fragments/ in my next blog.

Software for recombination detection:

RAT http://cbr.jic.ac.uk/dicks/software/RAT/

Breakpointer https://github.com/ruping/Breakpointer

DRP http://web.cbio.uct.ac.za/~darren/rdp.html

RB-finder http://www.ncbi.nlm.nih.gov/pubmed/18707535

LDhat2.0 http://ldhat.sourceforge.net/LDhat2.0/instructions.shtml

Reference:

http://www.nature.com/scitable/topicpage/genetic-recombination-514#

Image: Wikipedia , sciencelearn.org.nz

Recommended Articles:

http://www.friendshipcircle.org/blog/2012/05/22/13-chromosomal-disorders-youve-never-heard-of/

http://web.udl.es/usuaris/e4650869/docencia/segoncicle/genclin98/recursos_classe_%28pdf%29/revisionsPDF/chromosyndromes.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775595/table/T2/

http://learn.genetics.utah.edu/content/disorders/chromosomal/

http://www.ncert.nic.in/html/learning_basket/biology/cc&cd.pdf

EAGER

Jit — Sat, 10 Dec 2016 18:07:23 -0600

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.

EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0918-z

Address of the bookmark: https://github.com/apeltzer/EAGER-GUI