Publicly available tools and open resources in Bioinformatics

Feb 1, 201612 likes7,357 views

This document provides an overview of several freely available bioinformatics tools and open resources. It describes the purpose and function of popular tools for database searching (BLAST, FASTA), sequence alignment (Clustal Omega), visualization (RasMol), molecular dynamics simulation (GROMACS), genome browsing (Ensembl), and protein modeling (MODELLER). These tools are commonly used for tasks like extracting meaningful biological information from databases, comparing sequences, understanding phylogenetic relationships, displaying molecular structures, simulating protein dynamics, and building protein models. The document provides links to each tool's homepage for further information.

Publicly available tools
&
open resources
in
BIOINFORMATICS
Arindam Ghosh
ag1805xag1805x

Bioinformatics tools
● These are software programs that are designed
for extracting the meaningful information from
the mass of molecular biology / biological
databases & to carry out sequence or structural
analysis.
● Major categories of Bioinformatics Tools :
● Homology and Similarity Tools
● Protein Function Analysis
● Structural Analysis
● Sequence Analysis

BLAST
(http://blast.ncbi.nlm.nih.gov/Blast.cgi)
● Category: Database search
● BLAST=Basic Local Alignment
Search Tool
● It finds regions of local similarity
between sequences.
● Developed by NCBI
● It compares nucleotide or protein
sequences to sequence
databases and calculates the
statistical significance of matches.

FASTA
(http://www.ebi.ac.uk/Tools/sss/fasta)
●Category: Database search
●Alternate to NCBI-BLAST
●Suite of programs for searching nucleotide or
protein databases with a query sequence.
●FASTX and FASTY translate a nucleotide query
for searching a protein database.
●TFASTX and TFASTY translate a nucleotide
database to be searched with a protein query.

Clustal Omega
(http://www.clustal.org/omega/)
●Category: Sequence Alignment
●Multiple Sequence Alignment tool (MSA)
i.e. it aligns three or more sequences
together.
●Developed by the CLUSTAL authors at
University College Dublin, Ireland
●Standalone command line-only tool but is
also offered by webservers as of EMBL.
●MSA can be used to find conserved
sequences and understand phylogenetic
relations.

RasMol (http://www.openrasmol.org/)
●Category: Visualisation
●Developed by Roger Sayle
●Used to display proteins, nucleic acids and
small molecules
●The program reads in a molecule coordinate file
and interactively displays the molecule on the
screen in a variety of colour schemes and
molecule representations

GROMACS (http://www.gromacs.org/)
●Category: Molecular dynamics (simulation)
●GROMACS=GROningen MAchine for Chemical
Simulations
●Designed for simulations of proteins, lipids and
nucleic acids.
●Developed in the Biophysical Chemistry
department of University of Groningen
●GROMACS is operated via the command-line,
and can use files for input and output.

Ensembl (http://www.ensembl.org/index.html)
● Category: Genome Browser
● Genome browser is a graphical interface for display of
information from a biological database for genomic data.
● It enable researchers to visualize and browse entire
genomes (most have many complete genomes) with
annotated data including gene prediction and structure,
proteins, expression, regulation, variation, comparative
analysis, etc
● It is a joint scientific project between the European
Bioinformatics Institute and the Wellcome Trust Sanger
Institute

MODELLER
(http://salilab.org/modeller/)
●Category: Protein Modelling
●Used for producing homology models of protein
tertiary structures as well as quaternary
structures.
●MODELLER was originally written and is
currently maintained by Andrej Sali at the
University of California, San Francisco.

Few more tools....
●Database search- SSEARCH, AB-BLAST, PSI-Search
●Sequence alignment- T-Coffee, Sim4, Exonerate,
Bioconductor- Biostrings
●Visualization- Jmol, PyMOL, Visual Molecular
Dynamics
●Molecular dynamics- AMBER, CHARMM, Abalone
●Genome browser- Argo Genome Browser, Celera
Genome Browser, GenomeView
●Protein modelling- SWISS-MODEL, WHAT IF,
BHAGEERATH-H

This document provides an overview of structural bioinformatics and protein structure. It discusses the basics of protein structure including the primary, secondary, tertiary, and quaternary levels. Methods for determining three-dimensional protein structure such as X-ray crystallography and NMR spectroscopy are described. The document also covers protein structure visualization tools, comparison of protein structures to determine evolutionary relationships, and classification databases like SCOP and CATH. The key applications of structural bioinformatics are structure-based function prediction and aiding structural genomics projects.

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This document provides an overview of the field of bioinformatics. It defines bioinformatics as the intersection of biology and computer science, using computational tools to analyze and distribute biological information like DNA, RNA, and proteins. The goals of bioinformatics are to better understand cells at the molecular level by analyzing sequence and structure data. Key applications include drug design, DNA analysis, and agricultural biotechnology. The document also describes different types of biological databases like primary databases that contain raw sequence data, and secondary databases that provide additional annotation and analysis of sequences.

Bioinformatics data miningSangeeta Das

Data mining involves using machine learning and statistical methods to discover patterns in large datasets and is useful in bioinformatics for analyzing biological data. Bioinformatics analyzes data from sequences, molecules, gene expressions, and pathways. Data mining can help understand these rapidly growing biological datasets. Common data mining tools in bioinformatics include BLAST for sequence comparisons, Entrez for integrated database searching, and ORF Finder for identifying open reading frames. Data mining approaches are well-suited to the enormous volumes of data in bioinformatics databases.

Protein Structure, Databases and Structural AlignmentSaramita De Chakravarti

Protein structures can be aligned and compared using computational methods like structural alignment. Structural alignment finds the optimal rotation and translation that superimposes one protein structure onto another to maximize structural similarity. This is done by treating protein structures as sets of points defined by atom coordinates and finding the transformation that minimizes the root-mean-square deviation between corresponding atoms in the two structures. While useful, structural alignment has limitations like not accounting for differences in amino acid attributes and treating all atoms equally.

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Molecular modeling database Jayati Shrivastava

The Molecular Modeling Database (MMDB) is a database hosted by the National Center for Biotechnology Information that contains over 28,000 experimentally determined 3D structures of biomolecules including proteins and nucleic acids derived from the Protein Data Bank, excluding theoretical models. It facilitates computation and links structures to other data types. Each record cross-references its source PDB file. The database contains molecular structures, biological activity data, experimental data, chemical properties, and annotations to aid researchers. Examples of widely used molecular modeling databases discussed are the Protein Data Bank, PubChem, and RCSB Ligand Explorer.

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UniProt is a comprehensive, freely accessible database that is a central repository for protein data. It is produced through collaboration between the European Bioinformatics Institute, Swiss Institute of Bioinformatics, and Protein Information Resource. UniProt contains protein sequences, functional information, evolutionary data, and details about biological processes, post-translational modifications, interactions, and subcellular locations to characterize proteins.

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Swiss PROT Vidya Kalaivani Rajkumar

EMBL- European Molecular Biology LaboratoryThapar Institute of Engineering & Technology, Patiala, Punjab, India

SWISS-PROTThapar Institute of Engineering & Technology, Patiala, Punjab, India

SWISS-PROT is a curated protein sequence database that provides a high level of annotation and low redundancy. It contains information on the sequence, structure, function, and modifications of proteins. The database is maintained by the European Bioinformatics Institute and Swiss Institute of Bioinformatics. It integrates with other databases containing structural, domain, post-translational, and disease information.

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NCBI National Center for Biotechnology InformationThapar Institute of Engineering & Technology, Patiala, Punjab, India

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1) Pairwise sequence alignment is a method to compare two biological sequences like DNA, RNA, or proteins. It involves arranging the sequences in columns to highlight their similarities and differences. 2) There are many possible alignments between two sequences, but most imply too many mutations. The best alignment minimizes the number of mutations needed to explain the differences between the sequences. 3) For short protein sequences like "QKGSYPVRSTC" and "QKGSGPVRSTC", the optimal alignment implies one single mutation occurred since the sequences diverged from a common ancestor.

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The SCOP database classifies protein structures hierarchically and describes evolutionary relationships between proteins. It was created in 1994 at the Centre for Protein Engineering and is maintained manually. SCOP links to the Protein Data Bank to obtain structural classifications for each protein structure directly and can also be searched to find a protein's structural class, fold, and domain information.

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EMBLVidya Kalaivani Rajkumar

The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 22 member states. EMBL was created in 1974 and operates from five sites, performing basic research in molecular biology and molecular medicine. A key function of EMBL is the EMBL Nucleotide Sequence Database, maintained at the European Bioinformatics Institute, which incorporates and distributes nucleotide sequences from public sources as part of an international collaboration.

Fastauniversity of education,Lahore

This document provides an overview of the FASTA software. FASTA is a program used by biologists to study and analyze DNA and protein sequences. It uses a simple text-based format to present sequences and allows for the naming of sequences and inclusion of comments. FASTA is a rapid program that can be used locally or through email servers to find regional similarities between sequences and identify potential matches while ignoring complete sensitivity. It has become a standard tool in biology for sequencing and analyzing proteins and DNA.

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The document discusses the National Center for Biotechnology Information (NCBI), which maintains biological databases and provides bioinformatics tools. NCBI houses both primary databases directly submitted by researchers and secondary databases compiled from primary sources. Major databases include GenBank (nucleotide sequences), PubMed Central (biomedical literature), and reference sequence databases. Tools like BLAST, Entrez, and ORFfinder allow users to search and analyze sequence data. NCBI aims to make biomedical research data freely accessible worldwide.

Protein information resource (PIR)ShivaniShewale2

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UniProt is a comprehensive database of protein sequences and functional information that is curated by the European Bioinformatics Institute, SIB Swiss Institute of Bioinformatics, and the Protein Information Resource. It contains three main components: UniProtKB for functional information, UniRef for clustered sequences, and UniParc for comprehensive protein sequences. As genome sequencing increases, UniProt provides centralized storage and interconnection of protein data from various sources to further scientific understanding of proteins.

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This document discusses sequence alignment and the differences between global and local alignment. It defines sequence alignment as comparing two or more sequences to find identical or similar characters in the same order. Global alignment attempts to align the entire sequences, while local alignment finds the regions of highest similarity that may only be part of the sequences. Dynamic programming is used to calculate optimal alignments through initialization of a scoring matrix, filling it, and tracing back the highest scores. The Needleman-Wunch algorithm performs global alignment, while Smith-Waterman performs local alignment by setting negative scores to zero to terminate early alignments.

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Monte Carlo simulations and molecular dynamics simulations are common computational methods to study membrane proteins and lipid bilayers. Monte Carlo simulations use random sampling to explore the behavior of complex systems. Molecular dynamics simulations numerically simulate particle motions under internal and external forces based on empirical energy functions. There are different levels of molecular dynamics simulations including atomistic, united atom, and coarse grained simulations, each with varying degrees of atomic detail and accessible timescales. Parameterized force fields are used to model interactions in lipid and protein systems. These computational methods provide insights into membrane and protein dynamics that are difficult to obtain experimentally.

Freshers day anchoring scriptArindam Ghosh

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Ab initio protein structure prediction uses computational methods to predict a protein's 3D structure from its amino acid sequence. It relies on conformational searching to generate structure decoys and selecting native-like models. The key factors for success are an accurate energy function, efficient search methods like molecular dynamics or genetic algorithms, and effective selection of models close to the native structure. Model selection approaches include energy evaluations, compatibility scores, clustering of similar decoys, and identifying the lowest energy conformations.

Artificial VectorsArindam Ghosh

Artificial vectors such as bacterial artificial chromosomes (BACs), yeast artificial chromosomes (YACs), P1-derived artificial chromosomes (PACs), and human artificial chromosomes (HACs) can carry large DNA fragments for research purposes. BACs can hold up to 300kb of DNA and are used to sequence genomes. YACs can carry 500kb of DNA but are prone to rearrangement. HACs are separate microchromosomes that act as new chromosomes and can carry therapeutic genes for research including disease models.

Pseudo codeArindam Ghosh

Pseudo code is an informal way to describe the steps of an algorithm using a language-like syntax that is easier for humans to understand than formal code. It omits implementation details like variable declarations and uses natural language to describe control structures and function calls. Pseudo code is used in textbooks and publications to explain algorithms to programmers of different languages, and by programmers to plan code before implementation. Common elements borrowed from languages include loops, conditionals, and basic syntax, but there is no standard form.

Hamiltonian pathArindam Ghosh

This document discusses the Hamiltonian path problem in graph theory. A Hamiltonian path visits each vertex in a graph exactly once. The Hamiltonian path problem is determining if a Hamiltonian path exists in a given graph. It is computationally difficult to solve and several algorithms have been developed, including brute force search, dynamic programming, and Monte Carlo algorithms. Unconventional models of computing like DNA computers have also been used to attempt solving the Hamiltonian path problem by exploiting parallel chemical reactions.

MySQL and bioinformatics Arindam Ghosh

The document discusses how MySQL provides an efficient database management system for storing vast amounts of biological data generated by advances in molecular biology techniques and projects like the Human Genome Project. It describes MySQL's architecture including layers for applications, logical queries and transactions, and storage management. MySQL is an open-source relational database widely used for biological data storage and querying due to its performance and ease of use.

Protein sorting in mitochondriaArindam Ghosh

Mitochondria contain proteins encoded by both their own genome and the nuclear genome. Newly synthesized nuclear-encoded proteins contain targeting signals that direct them to the mitochondria. There are several pathways that transport mitochondrial proteins across the outer and inner membranes and sort them to their correct submitochondrial compartment - the outer membrane, intermembrane space, inner membrane, or matrix. Protein translocases like TOM, TIM23, and TIM22 recognize different targeting signals and mediate the transport and sorting of precursor proteins to their proper destinations.

Network embedding in biomedical data scienceArindam Ghosh

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Pharmacogenomics & its ethical issuesArindam Ghosh

Carbon NanotubesArindam Ghosh

Monte Carlo Simulations & Membrane Simulation and DynamicsArindam Ghosh

Freshers day anchoring scriptArindam Ghosh

Ab Initio Protein Structure PredictionArindam Ghosh

Artificial VectorsArindam Ghosh

Pseudo codeArindam Ghosh

Hamiltonian pathArindam Ghosh

MySQL and bioinformatics Arindam Ghosh

Protein sorting in mitochondriaArindam Ghosh

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Publicly available tools and open resources in Bioinformatics

1. Publicly available tools & open resources in BIOINFORMATICS Arindam Ghosh ag1805xag1805x

2. Bioinformatics tools ● These are software programs that are designed for extracting the meaningful information from the mass of molecular biology / biological databases & to carry out sequence or structural analysis. ● Major categories of Bioinformatics Tools : ● Homology and Similarity Tools ● Protein Function Analysis ● Structural Analysis ● Sequence Analysis

3. BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) ● Category: Database search ● BLAST=Basic Local Alignment Search Tool ● It finds regions of local similarity between sequences. ● Developed by NCBI ● It compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

4. BLAST homepage

5. Nucleotide BLAST page

6. BLAST result page

7. BLAST result page continuation

8. FASTA (http://www.ebi.ac.uk/Tools/sss/fasta) ●Category: Database search ●Alternate to NCBI-BLAST ●Suite of programs for searching nucleotide or protein databases with a query sequence. ●FASTX and FASTY translate a nucleotide query for searching a protein database. ●TFASTX and TFASTY translate a nucleotide database to be searched with a protein query.

9. FASTA homepage

10. FASTA result page

11. FASTA result page

12. Clustal Omega (http://www.clustal.org/omega/) ●Category: Sequence Alignment ●Multiple Sequence Alignment tool (MSA) i.e. it aligns three or more sequences together. ●Developed by the CLUSTAL authors at University College Dublin, Ireland ●Standalone command line-only tool but is also offered by webservers as of EMBL. ●MSA can be used to find conserved sequences and understand phylogenetic relations.

13. Clustal Omega Homepage

14. Clustal Omega result page

15. Clustal Omega result page contd.

16. RasMol (http://www.openrasmol.org/) ●Category: Visualisation ●Developed by Roger Sayle ●Used to display proteins, nucleic acids and small molecules ●The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations

17. Different molecular views on RasMol

18. GROMACS (http://www.gromacs.org/) ●Category: Molecular dynamics (simulation) ●GROMACS=GROningen MAchine for Chemical Simulations ●Designed for simulations of proteins, lipids and nucleic acids. ●Developed in the Biophysical Chemistry department of University of Groningen ●GROMACS is operated via the command-line, and can use files for input and output.

19. Ensembl (http://www.ensembl.org/index.html) ● Category: Genome Browser ● Genome browser is a graphical interface for display of information from a biological database for genomic data. ● It enable researchers to visualize and browse entire genomes (most have many complete genomes) with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc ● It is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute

20. Ensemble homepage

21. Ensemble result page

22. Ensemble result page

23. MODELLER (http://salilab.org/modeller/) ●Category: Protein Modelling ●Used for producing homology models of protein tertiary structures as well as quaternary structures. ●MODELLER was originally written and is currently maintained by Andrej Sali at the University of California, San Francisco.

24. Modeller Homepage

25. Few more tools.... ●Database search- SSEARCH, AB-BLAST, PSI-Search ●Sequence alignment- T-Coffee, Sim4, Exonerate, Bioconductor- Biostrings ●Visualization- Jmol, PyMOL, Visual Molecular Dynamics ●Molecular dynamics- AMBER, CHARMM, Abalone ●Genome browser- Argo Genome Browser, Celera Genome Browser, GenomeView ●Protein modelling- SWISS-MODEL, WHAT IF, BHAGEERATH-H

26. THANK YOU ag1805xag1805x

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