Difference between revisions of "VT Genome analysis and protein folding support"
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*Next meeting: | *Next meeting: | ||
*Previous meetings (from scoping phase): 22th January 2014; 5th February 2014; Thursday 20th February 2014; 12th March 2014 12:00 CET; 27th March 2014 at 14:00 CET | *Previous meetings (from scoping phase): 22th January 2014; 5th February 2014; Thursday 20th February 2014; 12th March 2014 12:00 CET; 27th March 2014 at 14:00 CET | ||
Revision as of 13:24, 3 April 2014
General Project Information
- Leader:
- Meetings:
- Mailing List:
- Status: Under scoping
- Start Date: N.A.
- Duration: N.A.
- Next meeting:
- Previous meetings (from scoping phase): 22th January 2014; 5th February 2014; Thursday 20th February 2014; 12th March 2014 12:00 CET; 27th March 2014 at 14:00 CET
- Project Initiation document, minutes and presentations:https://documents.egi.eu/document/2149
Motivation
This proposal of virtual team project aims to integrate users and applications from the Sequencing and protein folding communities with EGI. At this moment we are collecting the information available within the different NGIs and compiling a use case list. This list includes the tools used and required by the community and will be used to fuel brainstorming and the definition of the tasks and outcomes.
Objectives
Identification of synergies between EGI and the communities of Sequencing and Protein Folding for future multidisciplinary projects-
Tasks
- Collect and analyze use cases dedicated to sequencing and protein folding in the different NGIs
- Build a table with the tools used / required by these communities
Members
EGI.eu
- Gergely Sipos, EGI.eu, Netherlands
- Nuno Ferreira EGI.eu, Netherlands
Portugal
- Afonso Duarte, EGI Champion
- Gonçalo Borges, LIP, IberGrid
Greece
- Fotis E. Psomopoulos, EGI Champion
- Kostas Koumantarosm, GRNet
Italy
- Daniele Cesini, INFN
France
- Johan Montagnatm, CNRS, LSGC
- Tiphaine Martin, KCL
Spain
- Ignacio Blanquer, UPVLC
Finland
- Kimmo Mattila, CSC
Germany
- Konrad Förster, IMIB
Others ? YOU ! (if interested in this potential virtual team email aduarte@itqb.unl.pt)
Resources
- NGI-Community engagement table: https://documents.egi.eu/document/2074.
Progress
- List of tools used/required by the sequencing and protein folding communities (see table below).
To add/change entries please use: https://docs.google.com/spreadsheet/ccc?key=0Ama69JoAAogvdHFzQi1UamwxN0MtVS1GUEV4ZmVGWXc&usp=sharing. If you don't have permission to do so please let us know!
- Presentations of the different NGIs with information on use cases: https://drive.google.com/folderview?id=0B2a69JoAAogvWUw2UG9KTWpydFE&usp=sharing.
List of tools used/required by the sequencing and protein folding communities
This list is a contribution from the different NGIs, users, developers, ...
If want to add/change entries please use the file (https://docs.google.com/spreadsheet/ccc?key=0Ama69JoAAogvdHFzQi1UamwxN0MtVS1GUEV4ZmVGWXc&usp=sharing).
If you don't have permission to do so please let contact us !
P.S.: This is a work in progress table
Name | type of tool (Application, workflow...) | Target Community(ies) |
Description |
Available in AppDB? | AppDB URL | Available online ? | website | Developer | Open source |
---|---|---|---|---|---|---|---|---|---|
Gromacs | Application | Protein structure, protein folding and protein dynamics | Performs molecular dynamics i.e calculate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS can work with different biochemical molecules (e.g. proteins, lipids and nucleic acids) | yes | https://appdb.egi.eu/store/software/gromacs.wenmr | yes | http://www.gromacs.org/ | http://www.gromacs.org/ | yes |
BLAST | Application | Bioinformatics, General Application, Basic Local Sequence Alignment | BLAST is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. | yes | https://appdb.egi.eu/store/software/blast | ||||
BiG (BLAST in Grids) | Application | Bioinformatics, General Application, Basic Local Sequence Alignment | To draw a comparison by BLAST between all sequences of prokaryotes, fungi, plants and animals The objective of this project, to run an application on the Grid infrastructure provided by the e-Science network, is to be able to launch BLAST processes in that infrastructure. More precisely, it is to draw a comparison by BLAST between all sequences of prokaryotes, fungi, plants and animals. The results are then analyzed using scripts to estimate the degree of horizontal transfer of genes between prokaryotes and plants. To do so, those proteins that are found in prokaryotes and plants but not in animals will be identified, using different similarity thresholds to consider to what extent the similarity between two proteins implies a common origin or not. |
yes | https://appdb.egi.eu/store/software/big.blast.in.grids | ||||
BWA Burrows-Wheeler Aligner | Application | Bioinformatics, General Application, Next Generation Sequence Assembling | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short a nd BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. |
yes | https://appdb.egi.eu/store/software/bwa.burrows.wheeler.aligner | ||||
VELVET | Application | Bioinformatics, General Application, Next Generation Sequence Assembling | Sequence assembler for very short reads Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. |
yes | https://appdb.egi.eu/store/software/velvet | ||||
SOAP-denovo | Application | Bioinformatics, General Application, Next Generation Sequence Assembling | SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. |
yes | https://appdb.egi.eu/store/software/soap.denovo | ||||
ClustalW-MPI | Application | Bioinformatics, General Application, Multiple Sequence Alignment | ClustalW parallel implementation ClustalW is a tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is a distributed and parallel implementation of ClustalW. All three steps have been parallelized to reduce the execution time. |
yes | https://appdb.egi.eu/store/software/clustalw.mpi | ||||
CLUSTALW | Application | Bioinformatics, General Application, Multiple Sequence Alignment | ClustalW is a program to perform multiple alignment of nucleic acid and protein sequences | yes | https://appdb.egi.eu/store/software/clustalw.mpi | ||||
MAFFT | Application | Bioinformatics, General Application, Multiple Sequence Alignment | Multiple Alignment using Fast Fourier Transform MAFFT is a multiple alignment program for amino acid or nucleotide sequences |
yes | https://appdb.egi.eu/store/software/mafft | ||||
MUSCLE | Application | Bioinformatics, General Application, Multiple Sequence Alignment | MUltiple Sequence Comparison by Log-Expectation MUSCLE is public domain multiple alignment software for protein and nucleotide sequences |
yes | https://appdb.egi.eu/store/software/muscle | ||||
HMMER | Application | Bioinformatics, General Application, Multiple Sequence Alignment | Profile hidden Markov models (profile HMMs) can be used to do sensitive database... Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family’s consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis |
yes | https://appdb.egi.eu/store/software/hmmer | ||||
MrBayes | Application | Bioinformatics, General Application, Phylogenetics | A program for the Bayesian estimation of phylogeny The reconstruction of the evolutionary history of a group of organisms (phylogeny) is used throughout the life science, as they offer a structure around which to organize the knowledge and data accumulated by researchers. The inference of phylogenies with computational methods is widely used in medical and biological research and has many important applications, such as gene commonly prediction, drug discovery and conservation biology. The most commonly used methods to infer phylogenies include cladistics, phenetics, maximum likelihood and Markov Chain Monte Carlo based Bayesian inference. These last two depend upon a mathematical model describing the evolution of characters observed in the species included and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequence. Due to the nature of Bayesian inference, the simulation can be prone to entrapment in local optima. To overcome this problem and achieve better estimation, the MrBayes program has to run for millions of iterations (generations) which require a large amount of computation time. For multiple sessions with different models or parameters, it will take a long time before the results can be analyzed and summarized. Since the phylogenetic tools are widely used by bioinformatics community, a Grid service for the parallelised version of MrBayes application has been deployed in order to allow bioinformatics to perform phylogenetic studies on a large scale. |
yes | https://appdb.egi.eu/store/software/mrbayes | ||||
CD-HIT-Grid | Application | Bioinformatics, General Application, Sequence Analysis | Protein clustering on the Grid with CD-HIT CD-HIT performs protein clustering on a protein or genome sequence database. This consists in removing redundant sequences at a given sequence similarity level and generating a new database with the representatives only. As protein and genome databases are growing up day after day, the clustering process on interesting datasets in a single machine is not feasible due to memory constrains. A Grid environment allows an adaptive database distribution in order to optimize its overall analysis. This activity was proposed by CNIO (Spanish National Cancer Research Centre) and started in the context of the BioGridNet Program |
yes | https://appdb.egi.eu/store/software/cd.hit.grid | ||||
InterProScan | Application | Bioinformatics, General Application, Sequence Analysis | InterProScan is a tool that combines several types of analysis in order to assign one or more functional signatures to a particular protein. InterProScan is a tool that combines several types of analysis in order to assign one or more functional signatures to a particular protein. It is implemented as a wrapper for some applications that can be executed simultaneously and combined in a computational analysis. The application was ported within the framework of the FP7 EDGeS project |
yes | https://appdb.egi.eu/store/software/interproscan | ||||
Grid Bio Portal (GISELA) | Platform | Bioinformatics, Sequence Analysis | Grid Portal of Bioinformatics Applications The application consists on a Grid Portal in which different bioinformatics applications can be deployed. Different Grid services implement basic tools such as multiple alignments, Phylogenetics inference, etc, which run on a Grid infrastructure, along with more complex compound workflows that implement widely used analysis sequences. The portal will provide authentication, load balancing, session management, workflow, user interface, reliability, fault tolerance, data management and accounting. This software layer will increase the productivity of software production cycle and will offer a uniform framework to host Grid services. The portal will run on a computer provided of a Grid User Interface, acting as a bridge between the Web and the Grid sides. It makes use of myproxy servers and all the other global Grid Services (data catalogue, resource brokering, file transfer, etc.). |
yes | https://appdb.egi.eu/store/software/grid.bio.portal.gisela | ||||
EMBOSS_in_JST | Application, Platform | Bioinformatics, Sequence Analysis | The European Molecular Biology Open Software Suite in the JST framework EMBOSS, ”The European Molecular Biology Open Software Suite” is a free Open Source software analysis package well established in the world-wide bioinformatics community. The tool has been adapted to be executed on the EGEE grid infrastructure within the JST framework in order to perform large scale analyses. Compared to other porting of the EMBOSS package on the GRID environment such as GrEMBOSS (http://cimi.ccg.unam.mx/ccg-OrganicG/en/GrEMBOSS), a gridified version of EMBOSS developed inside the EELA project, EMBOSS_in_JST appears to be well performing in the management of large data flow. The validity of the EMBOSS_in_JST approach was validated on a case study on Viroids. They are circular RNAs infecting plants. They show compact secondary structures and are unable to code for any protein. Infectivity of these RNAs exclusively relies on their ability to interact directly with host factors (proteins and/or RNAs) and to redirect cellular machinery and biosynthetic pathways for their replication and spread in the host. Viroids accomplish this aim likely mimicking some host RNA structural property. Therefore, viroid RNAs may unveil structural motives with functional properties also contained in cellular RNAs. Bioinformatics approaches in viroid research are impaired by the fact that the complete genome of most natural viroid hosts is still unknown. To overcome this difficulty we decided to run a secondary structure analysis on sub-sequences of the whole plant sequence data set available in EMBL. We analysed as a first test 231’000 intron regions for the secondary structure of interest by using the vrnalfold algorithm (search for local folding patterns) from the EMBOSS/EMBASSY package. |
yes | https://appdb.egi.eu/store/software/emboss.in.jst |