The FASTA Program Package Introduction
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T-Coffee Documentation Release Version 13.45.47.Aba98c5
T-Coffee Documentation Release Version_13.45.47.aba98c5 Cedric Notredame Aug 31, 2021 Contents 1 T-Coffee Installation 3 1.1 Installation................................................3 1.1.1 Unix/Linux Binaries......................................4 1.1.2 MacOS Binaries - Updated...................................4 1.1.3 Installation From Source/Binaries downloader (Mac OSX/Linux)...............4 1.2 Template based modes: PSI/TM-Coffee and Expresso.........................5 1.2.1 Why do I need BLAST with T-Coffee?.............................6 1.2.2 Using a BLAST local version on Unix.............................6 1.2.3 Using the EBI BLAST client..................................6 1.2.4 Using the NCBI BLAST client.................................7 1.2.5 Using another client.......................................7 1.3 Troubleshooting.............................................7 1.3.1 Third party packages......................................7 1.3.2 M-Coffee parameters......................................9 1.3.3 Structural modes (using PDB)................................. 10 1.3.4 R-Coffee associated packages................................. 10 2 Quick Start Regressive Algorithm 11 2.1 Introduction............................................... 11 2.2 Installation from source......................................... 12 2.3 Examples................................................. 12 2.3.1 Fast and accurate........................................ 12 2.3.2 Slower and more accurate.................................... 12 2.3.3 Very Fast........................................... -
How to Generate a Publication-Quality Multiple Sequence Alignment (Thomas Weimbs, University of California Santa Barbara, 11/2012)
Tutorial: How to generate a publication-quality multiple sequence alignment (Thomas Weimbs, University of California Santa Barbara, 11/2012) 1) Get your sequences in FASTA format: • Go to the NCBI website; find your sequences and display them in FASTA format. Each sequence should look like this (http://www.ncbi.nlm.nih.gov/protein/6678177?report=fasta): >gi|6678177|ref|NP_033320.1| syntaxin-4 [Mus musculus] MRDRTHELRQGDNISDDEDEVRVALVVHSGAARLGSPDDEFFQKVQTIRQTMAKLESKVRELEKQQVTIL ATPLPEESMKQGLQNLREEIKQLGREVRAQLKAIEPQKEEADENYNSVNTRMKKTQHGVLSQQFVELINK CNSMQSEYREKNVERIRRQLKITNAGMVSDEELEQMLDSGQSEVFVSNILKDTQVTRQALNEISARHSEI QQLERSIRELHEIFTFLATEVEMQGEMINRIEKNILSSADYVERGQEHVKIALENQKKARKKKVMIAICV SVTVLILAVIIGITITVG 2) In a text editor, paste all your sequences together (in the order that you would like them to appear in the end). It should look like this: >gi|6678177|ref|NP_033320.1| syntaxin-4 [Mus musculus] MRDRTHELRQGDNISDDEDEVRVALVVHSGAARLGSPDDEFFQKVQTIRQTMAKLESKVRELEKQQVTIL ATPLPEESMKQGLQNLREEIKQLGREVRAQLKAIEPQKEEADENYNSVNTRMKKTQHGVLSQQFVELINK CNSMQSEYREKNVERIRRQLKITNAGMVSDEELEQMLDSGQSEVFVSNILKDTQVTRQALNEISARHSEI QQLERSIRELHEIFTFLATEVEMQGEMINRIEKNILSSADYVERGQEHVKIALENQKKARKKKVMIAICV SVTVLILAVIIGITITVG >gi|151554658|gb|AAI47965.1| STX3 protein [Bos taurus] MKDRLEQLKAKQLTQDDDTDEVEIAVDNTAFMDEFFSEIEETRVNIDKISEHVEEAKRLYSVILSAPIPE PKTKDDLEQLTTEIKKRANNVRNKLKSMERHIEEDEVQSSADLRIRKSQHSVLSRKFVEVMTKYNEAQVD FRERSKGRIQRQLEITGKKTTDEELEEMLESGNPAIFTSGIIDSQISKQALSEIEGRHKDIVRLESSIKE LHDMFMDIAMLVENQGEMLDNIELNVMHTVDHVEKAREETKRAVKYQGQARKKLVIIIVIVVVLLGILAL IIGLSVGLK -
The ELIXIR Core Data Resources: Fundamental Infrastructure for The
Supplementary Data: The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences The “Supporting Material” referred to within this Supplementary Data can be found in the Supporting.Material.CDR.infrastructure file, DOI: 10.5281/zenodo.2625247 (https://zenodo.org/record/2625247). Figure 1. Scale of the Core Data Resources Table S1. Data from which Figure 1 is derived: Year 2013 2014 2015 2016 2017 Data entries 765881651 997794559 1726529931 1853429002 2715599247 Monthly user/IP addresses 1700660 2109586 2413724 2502617 2867265 FTEs 270 292.65 295.65 289.7 311.2 Figure 1 includes data from the following Core Data Resources: ArrayExpress, BRENDA, CATH, ChEBI, ChEMBL, EGA, ENA, Ensembl, Ensembl Genomes, EuropePMC, HPA, IntAct /MINT , InterPro, PDBe, PRIDE, SILVA, STRING, UniProt ● Note that Ensembl’s compute infrastructure physically relocated in 2016, so “Users/IP address” data are not available for that year. In this case, the 2015 numbers were rolled forward to 2016. ● Note that STRING makes only minor releases in 2014 and 2016, in that the interactions are re-computed, but the number of “Data entries” remains unchanged. The major releases that change the number of “Data entries” happened in 2013 and 2015. So, for “Data entries” , the number for 2013 was rolled forward to 2014, and the number for 2015 was rolled forward to 2016. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences 1 Figure 2: Usage of Core Data Resources in research The following steps were taken: 1. API calls were run on open access full text articles in Europe PMC to identify articles that mention Core Data Resource by name or include specific data record accession numbers. -
Dual Proteome-Scale Networks Reveal Cell-Specific Remodeling of the Human Interactome
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome Edward L. Huttlin1*, Raphael J. Bruckner1,3, Jose Navarrete-Perea1, Joe R. Cannon1,4, Kurt Baltier1,5, Fana Gebreab1, Melanie P. Gygi1, Alexandra Thornock1, Gabriela Zarraga1,6, Stanley Tam1,7, John Szpyt1, Alexandra Panov1, Hannah Parzen1,8, Sipei Fu1, Arvene Golbazi1, Eila Maenpaa1, Keegan Stricker1, Sanjukta Guha Thakurta1, Ramin Rad1, Joshua Pan2, David P. Nusinow1, Joao A. Paulo1, Devin K. Schweppe1, Laura Pontano Vaites1, J. Wade Harper1*, Steven P. Gygi1*# 1Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA. 2Broad Institute, Cambridge, MA, 02142, USA. 3Present address: ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, 02115, USA. 4Present address: Merck, West Point, PA, 19486, USA. 5Present address: IQ Proteomics, Cambridge, MA, 02139, USA. 6Present address: Vor Biopharma, Cambridge, MA, 02142, USA. 7Present address: Rubius Therapeutics, Cambridge, MA, 02139, USA. 8Present address: RPS North America, South Kingstown, RI, 02879, USA. *Correspondence: [email protected] (E.L.H.), [email protected] (J.W.H.), [email protected] (S.P.G.) #Lead Contact: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
To Find Information About Arabidopsis Genes Leonore Reiser1, Shabari
UNIT 1.11 Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes Leonore Reiser1, Shabari Subramaniam1, Donghui Li1, and Eva Huala1 1Phoenix Bioinformatics, Redwood City, CA USA ABSTRACT The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, orthologs gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, genome organization, images of mutant plants, protein sub-cellular localizations, publications, and the research community. The various data types are extensively interconnected and can be accessed through a variety of Web-based search and display tools. This unit primarily focuses on some basic methods for searching, browsing, visualizing, and analyzing information about Arabidopsis genes and genome, Additionally we describe how members of the community can share data using TAIR’s Online Annotation Submission Tool (TOAST), in order to make their published research more accessible and visible. Keywords: Arabidopsis ● databases ● bioinformatics ● data mining ● genomics INTRODUCTION The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource for the biology of Arabidopsis thaliana (Huala et al., 2001; Garcia-Hernandez et al., 2002; Rhee et al., 2003; Weems et al., 2004; Swarbreck et al., 2008, Lamesch, et al., 2010, Berardini et al., 2016). The TAIR database contains information about genes, proteins, gene expression, mutant phenotypes, germplasms, clones, genetic markers, genetic and physical maps, genome organization, publications, and the research community. In addition, seed and DNA stocks from the Arabidopsis Biological Resource Center (ABRC; Scholl et al., 2003) are integrated with genomic data, and can be ordered through TAIR. -
Sequence Motifs, Correlations and Structural Mapping of Evolutionary
Talk overview • Sequence profiles – position specific scoring matrix • Psi-blast. Automated way to create and use sequence Sequence motifs, correlations profiles in similarity searches and structural mapping of • Sequence patterns and sequence logos evolutionary data • Bioinformatic tools which employ sequence profiles: PFAM BLOCKS PROSITE PRINTS InterPro • Correlated Mutations and structural insight • Mapping sequence data on structures: March 2011 Eran Eyal Conservations Correlations PSSM – position specific scoring matrix • A position-specific scoring matrix (PSSM) is a commonly used representation of motifs (patterns) in biological sequences • PSSM enables us to represent multiple sequence alignments as mathematical entities which we can work with. • PSSMs enables the scoring of multiple alignments with sequences, or other PSSMs. PSSM – position specific scoring matrix Assuming a string S of length n S = s1s2s3...sn If we want to score this string against our PSSM of length n (with n lines): n alignment _ score = m ∑ s j , j j=1 where m is the PSSM matrix and sj are the string elements. PSSM can also be incorporated to both dynamic programming algorithms and heuristic algorithms (like Psi-Blast). Sequence space PSI-BLAST • For a query sequence use Blast to find matching sequences. • Construct a multiple sequence alignment from the hits to find the common regions (consensus). • Use the “consensus” to search again the database, and get a new set of matching sequences • Repeat the process ! Sequence space Position-Specific-Iterated-BLAST • Intuition – substitution matrices should be specific to sites and not global. – Example: penalize alanine→glycine more in a helix •Idea – Use BLAST with high stringency to get a set of closely related sequences. -
Orthofiller: Utilising Data from Multiple Species to Improve the Completeness of Genome Annotations Michael P
Dunne and Kelly BMC Genomics (2017) 18:390 DOI 10.1186/s12864-017-3771-x SOFTWARE Open Access OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations Michael P. Dunne and Steven Kelly* Abstract Backround: Complete and accurate annotation of sequenced genomes is of paramount importance to their utility and analysis. Differences in gene prediction pipelines mean that genome annotations for a species can differ considerably in the quality and quantity of their predicted genes. Furthermore, genes that are present in genome sequences sometimes fail to be detected by computational gene prediction methods. Erroneously unannotated genes can lead to oversights and inaccurate assertions in biological investigations, especially for smaller-scale genome projects, which rely heavily on computational prediction. Results: Here we present OrthoFiller, a tool designed to address the problem of finding and adding such missing genes to genome annotations. OrthoFiller leverages information from multiple related species to identify those genes whose existence can be verified through comparison with known gene families, but which have not been predicted. By simulating missing gene annotations in real sequence datasets from both plants and fungi we demonstrate the accuracy and utility of OrthoFiller for finding missing genes and improving genome annotations. Furthermore, we show that applying OrthoFiller to existing “complete” genome annotations can identify and correct substantial numbers of erroneously missing genes in these two sets of species. Conclusions: We show that significant improvements in the completeness of genome annotations can be made by leveraging information from multiple species. Keywords: Genome annotation, Gene prediction, Orthology, Orthogroup Background of several effective algorithms for identifying genes in Genome sequences have become fundamental to many de novo sequenced genomes [3]. -
The Biogrid Interaction Database
D470–D478 Nucleic Acids Research, 2015, Vol. 43, Database issue Published online 26 November 2014 doi: 10.1093/nar/gku1204 The BioGRID interaction database: 2015 update Andrew Chatr-aryamontri1, Bobby-Joe Breitkreutz2, Rose Oughtred3, Lorrie Boucher2, Sven Heinicke3, Daici Chen1, Chris Stark2, Ashton Breitkreutz2, Nadine Kolas2, Lara O’Donnell2, Teresa Reguly2, Julie Nixon4, Lindsay Ramage4, Andrew Winter4, Adnane Sellam5, Christie Chang3, Jodi Hirschman3, Chandra Theesfeld3, Jennifer Rust3, Michael S. Livstone3, Kara Dolinski3 and Mike Tyers1,2,4,* 1Institute for Research in Immunology and Cancer, Universite´ de Montreal,´ Montreal,´ Quebec H3C 3J7, Canada, 2The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada, 3Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, 4School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK and 5Centre Hospitalier de l’UniversiteLaval´ (CHUL), Quebec,´ Quebec´ G1V 4G2, Canada Received September 26, 2014; Revised November 4, 2014; Accepted November 5, 2014 ABSTRACT semi-automated text-mining approaches, and to en- hance curation quality control. The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein in- INTRODUCTION teractions curated from the primary biomedical lit- Massive increases in high-throughput DNA sequencing erature for all major model organism species and technologies (1) have enabled an unprecedented level of humans. As of September 2014, the BioGRID con- genome annotation for many hundreds of species (2–6), tains 749 912 interactions as drawn from 43 149 pub- which has led to tremendous progress in the understand- lications that represent 30 model organisms. -
Infravec2 Open Research Data Management Plan
INFRAVEC2 OPEN RESEARCH DATA MANAGEMENT PLAN Authors: Andrea Crisanti, Gareth Maslen, Andy Yates, Paul Kersey, Alain Kohl, Clelia Supparo, Ken Vernick Date: 10th July 2020 Version: 3.0 Overview Infravec2 will align to Open Research Data, as follows: Data Types and Standards Infravec2 will generate a variety of data types, including molecular data types: genome sequence and assembly, structural annotation (gene models, repeats, other functional regions) and functional annotation (protein function assignment), variation data, and transcriptome data; arbovirus and malaria experimental infection data, linked to archived samples; and microbiome data (Operational Taxonomic Units), including natural virome composition. All data will be released according to the appropriate standards and formats for each data type. For example, DNA sequence will be released in FASTA format; variant calls in Variant Call Format; sequence alignments in BAM (Binary Alignment Map) and CRAM (Compressed Read Alignment Map) formats, etc. We will strongly encourage the organisation of linked data sets as Track Hubs, a mechanism for publishing a set of linked genomic data that aids data discovery, sharing, and selection for subsequent analysis. We will develop internal standards within the consortium to define minimal metadata that will accompany all data sets, following the template of the Minimal Information Standards for Biological and Biomedical Investigations (http://www.dcc.ac.uk/resources/metadata-standards/mibbi-minimum-information-biological- and-biomedical-investigations). Data Exploitation, Accessibility, Curation and Preservation All molecular data for which existing public data repositories exist will be submitted to such repositories on or before the publication of written manuscripts, with early release of data (i.e. -
Introduction to Linux for Bioinformatics – Part II Paul Stothard, 2006-09-20
Introduction to Linux for bioinformatics – part II Paul Stothard, 2006-09-20 In the previous guide you learned how to log in to a Linux account, and you were introduced to some basic Linux commands. This section covers some more advanced commands and features of the Linux operating system. It also introduces some command-line bioinformatics programs. One important aspect of using a Linux system from a Windows or Mac environment that was not discussed in the previous section is how to transfer files between computers. For example, you may have a collection of sequence records on your Windows desktop that you wish to analyze using a Linux command-line program. Alternatively, you may want to transfer some sequence analysis results from a Linux system to your Mac so that you can add them to a PowerPoint presentation. Transferring files between Mac OS X and Linux Recall that Mac OS X includes a Terminal application (located in the Applications >> Utilities folder), which can be used to log in to other systems. This terminal can also be used to transfer files, thanks to the scp command. Try transferring a file from your Mac to your Linux account using the Terminal application: 1. Launch the Terminal program. 2. Instead of logging in to your Linux account, use the same basic commands you learned in the previous section (pwd, ls, and cd) to navigate your Mac file system. 3. Switch to your home directory on the Mac using the command cd ~ 4. Create a text file containing your home directory listing using ls -l > myfiles.txt 5. -
The Interpro Database, an Integrated Documentation Resource for Protein
The InterPro database, an integrated documentation resource for protein families, domains and functional sites R Apweiler, T K Attwood, A Bairoch, A Bateman, E Birney, M Biswas, P Bucher, L Cerutti, F Corpet, M D Croning, et al. To cite this version: R Apweiler, T K Attwood, A Bairoch, A Bateman, E Birney, et al.. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research, Oxford University Press, 2001, 29 (1), pp.37-40. 10.1093/nar/29.1.37. hal-01213150 HAL Id: hal-01213150 https://hal.archives-ouvertes.fr/hal-01213150 Submitted on 7 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. © 2001 Oxford University Press Nucleic Acids Research, 2001, Vol. 29, No. 1 37–40 The InterPro database, an integrated documentation resource for protein families, domains and functional sites R. Apweiler1,*, T. K. Attwood2,A.Bairoch3, A. Bateman4,E.Birney1, M. Biswas1, P. Bucher5, L. Cerutti4,F.Corpet6, M. D. R. Croning1,2, R. Durbin4,L.Falquet5,W.Fleischmann1, J. Gouzy6,H.Hermjakob1,N.Hulo3, I. Jonassen7,D.Kahn6,A.Kanapin1, Y. Karavidopoulou1, R. -
Lab 5: Bioinformatics I Sanger Sequence Analysis
Lab 5: Bioinformatics I Sanger Sequence Analysis Project Guide The Wolbachia Project 1 Arthropod Identification 2 DNA Extraction 3 PCR 4 Gel Electrophoresis 5 Bioinformatics Content is made available under the Creative Commons Attribution-NonCommercial-No Derivatives International License. Contact ([email protected]) if you would like to make adaptations for distribution beyond the classroom. The Wolbachia Project: Discover the Microbes Within! was developed by a collaboration of scientists, educators, and outreach specialists. It is directed by the Bordenstein Lab at Vanderbilt University. https://www.vanderbilt.edu/wolbachiaproject 2 Activity at a Glance Goal To analyze and interpret the quality of Sanger sequences, and generate a consensus DNA sequence for bioinformatics analyses. Learning Objectives Upon completion of this activity, students will (i) understand the Sanger method of sequencing, also known as the chain-termination method; (ii) be able to interpret chromatograms; (iii) evaluate sequencing Quality Scores; and (iv) generate a consensus DNA sequence based on forward and reverse Sanger reactions. Prerequisite Skills While no computer programming skills are necessary to complete this work, prior exposure to personal computers and the Internet is assumed. Teaching Time: One class period Recommended Background Tutorials • DNA Learning Center Animation: Sanger Method of DNA Sequencing (https://www.dnalc.org/view/15479-sanger-method-of-dna-sequencing-3d-animation-with- narration.html) • YouTube video: The Sanger