Bioinformatics Assignments for Introductory
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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 -
GCAT|Panel, a Comprehensive Structural Variant Haplotype Map of the Iberian Population from High-Coverage Whole-Genome Sequencing
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.20.453041; this version posted July 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing Jordi Valls-Margarit1,#, Iván Galván-Femenía2,3,#, Daniel Matías-Sánchez1,#, Natalia Blay2, Montserrat Puiggròs1, Anna Carreras2, Cecilia Salvoro1, Beatriz Cortés2, Ramon Amela1, Xavier Farre2, Jon Lerga- Jaso4, Marta Puig4, Jose Francisco Sánchez-Herrero5, Victor Moreno6,7,8,9, Manuel Perucho10,11, Lauro Sumoy5, Lluís Armengol12, Olivier Delaneau13,14, Mario Cáceres4,15, Rafael de Cid2,*,† & David Torrents1,15,* 1. Life sciences dept, Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain. 2. Genomes for Life-GCAT lab Group, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, 08916, Spain. 3. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain (current affiliation). 4. Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain. 5. High Content Genomics and Bioinformatics Unit, Institute for Health Science Research Germans Trias i Pujol (IGTP), 08916, Badalona, Spain. 6. Catalan Institute of Oncology, Hospitalet del Llobregat, 08908, Spain. 7. Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet del Llobregat, 08908, Spain. 8. CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, 28029, Spain. 9. Universitat de Barcelona (UB), Barcelona, 08007, Spain. -
GCAT (NM 014291) Human Tagged ORF Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RG204870 GCAT (NM_014291) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: GCAT (NM_014291) Human Tagged ORF Clone Tag: TurboGFP Symbol: GCAT Synonyms: KBL Vector: pCMV6-AC-GFP (PS100010) E. coli Selection: Ampicillin (100 ug/mL) Cell Selection: Neomycin ORF Nucleotide >RG204870 representing NM_014291 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGTGGCCTGGGAACGCCTGGCGCGCCGCACTCTTCTGGGTGCCCCGCGGCCGCCGCGCACAGTCAGCGC TGGCCCAGCTGCGTGGCATTCTGGAGGGGGAGCTGGAAGGCATCTGCGGAGCTGGCACTTGGAAGAGTGA GCGGGTCATCACGTCCCGTCAGGGGCCGCACATCCGCGTGGACGGCGTCTCCGGAGGAATCCTTAACTTC TGTGCCAACAACTACCTGGGCCTGAGCAGCCACCCTGAGGTGATCCAGGCAGGTCTGCAGGCTCTGGAGG AGTTTGGAGCTGGCCTCAGCTCTGTCCGCTTTATCTGTGGAACCCAGAGCATCCACAAGAATCTAGAAGC AAAAATAGCCCGCTTCCACCAGCGGGAGGATGCCATCCTCTATCCCAGCTGTTATGACGCCAACGCCGGC CTCTTTGAGGCCCTGCTGACCCCAGAGGACGCAGTCCTGTCGGACGAGCTGAACCATGCCTCCATCATCG ACGGCATCCGGCTGTGCAAGGCCCACAAGTACCGCTATCGCCACCTGGACATGGCCGACCTAGAAGCCAA GCTGCAGGAGGCCCAGAAGCATCGGCTGCGCCTGGTGGCCACTGATGGGGCCTTTTCCATGGATGGCGAC ATCGCACCCCTGCAGGAGATCTGCTGCCTCGCCTCTAGATATGGTGCCCTGGTCTTCATGGATGAATGCC ATGCCACTGGCTTCCTGGGGCCCACAGGACGGGGCACAGATGAGCTGCTGGGTGTGATGGACCAGGTCAC CATCATCAACTCCACCCTGGGGAAGGCCCTGGGTGGAGCATCAGGGGGCTACACGACAGGGCCTGGGCCC CTGGTGTCCCTGCTGCGGCAGCGCGCCCGGCCATACCTCTTCTCCAACAGTCTGCCACCTGCTGTCGTTG -
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. -
A Tool to Sanity Check and If Needed Reformat FASTA Files
bioRxiv preprint doi: https://doi.org/10.1101/024448; this version posted August 13, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Fasta-O-Matic: a tool to sanity check and if needed reformat FASTA files Jennifer Shelton Kansas State University August 11, 2015 Abstract As the shear volume of bioinformatic sequence data increases the only way to take advantage of this content is to more completely automate ro- bust analysis workflows. Analysis bottlenecks are often mundane and overlooked processing steps. Idiosyncrasies in reading and/or writing bioinformatics file formats can halt or impair analysis workflows by in- terfering with the transfer of data from one informatics tools to another. Fasta-O-Matic automates handling of common but minor format issues that otherwise may halt pipelines. The need for automation must be balanced by the need for manual confirmation that any formatting error is actually minor rather than indicative of a corrupt data file. To that end Fasta-O-Matic reports any issues detected to the user with optionally color coded and quiet or verbose logs. Fasta-O-Matic can be used as a general pre-processing tool in bioin- formatics workflows (e.g. to automatically wrap FASTA files so that they can be read by BioPerl). It was also developed as a sanity check for bioinformatic core facilities that tend to repeat common analysis steps on FASTA files received from disparate sources. -
Epigenetic Regulation of the Nuclear-Coded GCAT and SHMT2
www.nature.com/scientificreports OPEN Epigenetic regulation of the nuclear-coded GCAT and SHMT2 genes confers human Received: 29 October 2014 Accepted: 14 April 2015 age-associated mitochondrial Published: 22 May 2015 respiration defects Osamu Hashizume1,*, Sakiko Ohnishi1,*, Takayuki Mito1,*, Akinori Shimizu1, Kaori Ishikawa1, Kazuto Nakada1,2, Manabu Soda3, Hiroyuki Mano3, Sumie Togayachi4, Hiroyuki Miyoshi4,5, Keisuke Okita6 & Jun-Ichi Hayashi1,2,7 Age-associated accumulation of somatic mutations in mitochondrial DNA (mtDNA) has been proposed to be responsible for the age-associated mitochondrial respiration defects found in elderly human subjects. We carried out reprogramming of human fibroblast lines derived from elderly subjects by generating their induced pluripotent stem cells (iPSCs), and examined another possibility, namely that these aging phenotypes are controlled not by mutations but by epigenetic regulation. Here, we show that reprogramming of elderly fibroblasts restores age-associated mitochondrial respiration defects, indicating that these aging phenotypes are reversible and are similar to differentiation phenotypes in that both are controlled by epigenetic regulation, not by mutations in either the nuclear or the mitochondrial genome. Microarray screening revealed that epigenetic downregulation of the nuclear-coded GCAT gene, which is involved in glycine production in mitochondria, is partly responsible for these aging phenotypes. Treatment of elderly fibroblasts with glycine effectively prevented the expression of these -
A Tool to Sanity Check and If Needed Reformat FASTA Files
ManuscriptbioRxiv preprint doi: https://doi.org/10.1101/024448; this version posted August 21, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under Click here to download Manuscript: bmc_article.tex aCC-BY 4.0 International license. Click here to view linked References Shelton and Brown 1 2 3 4 5 RESEARCH 6 7 8 9 Fasta-O-Matic: a tool to sanity check and if 10 11 needed reformat FASTA files 12 13 Jennifer M Shelton1 and Susan J Brown1* 14 15 *Correspondence: [email protected] 16 1KSU/K-INBRE Bioinformatics Abstract 17 Center, Division of Biology, 18 Kansas State University, Background: As the sheer volume of bioinformatic sequence data increases, the 19 Manhattan, KS, USA only way to take advantage of this content is to more completely automate Full list of author information is 20 available at the end of the article robust analysis workflows. Analysis bottlenecks are often mundane and 21 overlooked processing steps. Idiosyncrasies in reading and/or writing 22 bioinformatics file formats can halt or impair analysis workflows by interfering 23 with the transfer of data from one informatics tools to another. 24 Results: Fasta-O-Matic automates handling of common but minor formatissues 25 that otherwise may halt pipelines. The need for automation must be balanced by 26 the need for manual confirmation that any formatting error is actually minor 27 28 rather than indicative of a corrupt data file. -
The FASTA Program Package Introduction
fasta-36.3.8 December 4, 2020 The FASTA program package Introduction This documentation describes the version 36 of the FASTA program package (see W. R. Pearson and D. J. Lipman (1988), “Improved Tools for Biological Sequence Analysis”, PNAS 85:2444-2448, [17] W. R. Pearson (1996) “Effective protein sequence comparison” Meth. Enzymol. 266:227- 258 [15]; and Pearson et. al. (1997) Genomics 46:24-36 [18]. Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and for evaluating statistical significance from randomly shuffled sequences. This document is divided into four sections: (1) A summary overview of the programs in the FASTA3 package; (2) A guide to using the FASTA programs; (3) A guide to installing the programs and databases. Section (4) provides answers to some Frequently Asked Questions (FAQs). In addition to this document, the changes v36.html, changes v35.html and changes v34.html files list functional changes to the programs. The readme.v30..v36 files provide a more complete revision history of the programs, including bug fixes. The programs are easy to use; if you are using them on a machine that is administered by someone else, you can focus on sections (1) and (2) to learn how to use the programs. If you are installing the programs on your own machine, you will need to read section (3) carefully. FASTA and BLAST – FASTA and BLAST have the same goal: to identify statistically signifi- cant sequence similarity that can be used to infer homology. The FASTA programs offer several advantages over BLAST: 1. -
Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins, Second Edition Andreas D
BIOINFORMATICS A Practical Guide to the Analysis of Genes and Proteins SECOND EDITION Andreas D. Baxevanis Genome Technology Branch National Human Genome Research Institute National Institutes of Health Bethesda, Maryland USA B. F. Francis Ouellette Centre for Molecular Medicine and Therapeutics Children’s and Women’s Health Centre of British Columbia University of British Columbia Vancouver, British Columbia Canada A JOHN WILEY & SONS, INC., PUBLICATION New York • Chichester • Weinheim • Brisbane • Singapore • Toronto BIOINFORMATICS SECOND EDITION METHODS OF BIOCHEMICAL ANALYSIS Volume 43 BIOINFORMATICS A Practical Guide to the Analysis of Genes and Proteins SECOND EDITION Andreas D. Baxevanis Genome Technology Branch National Human Genome Research Institute National Institutes of Health Bethesda, Maryland USA B. F. Francis Ouellette Centre for Molecular Medicine and Therapeutics Children’s and Women’s Health Centre of British Columbia University of British Columbia Vancouver, British Columbia Canada A JOHN WILEY & SONS, INC., PUBLICATION New York • Chichester • Weinheim • Brisbane • Singapore • Toronto Designations used by companies to distinguish their products are often claimed as trademarks. In all instances where John Wiley & Sons, Inc., is aware of a claim, the product names appear in initial capital or ALL CAPITAL LETTERS. Readers, however, should contact the appropriate companies for more complete information regarding trademarks and registration. Copyright ᭧ 2001 by John Wiley & Sons, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic or mechanical, including uploading, downloading, printing, decompiling, recording or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without the prior written permission of the Publisher. -
Need and Role of Scala Implementations in Bioinformatics
(IJACSA) International Journal of Advanced Computer Science and Applications, Vol. 8, No. 2, 2017 Need and Role of Scala Implementations in Bioinformatics Abbas Rehman Muhammad Atif Sarwar Department of Computer Science Department of Computer Science COMSATS Institute of Information Technology COMSATS Institute of Information Technology Sahiwal, Pakistan Sahiwal, Pakistan Ali Abbas Javed Ferzund Department of Computer Science Department of Computer Science COMSATS Institute of Information Technology COMSATS Institute of Information Technology Sahiwal, Pakistan Sahiwal, Pakistan Abstract—Next Generation Sequencing has resulted in the evolutionary change in data generation of different sequences. generation of large number of omics data at a faster speed that NGS machines are generating a huge amount of sequence data was not possible before. This data is only useful if it can be stored per day that needs to be stored, analyzed and managed well to and analyzed at the same speed. Big Data platforms and tools like seek the maximum advantages from this. Existing Apache Hadoop and Spark has solved this problem. However, bioinformatics techniques, tools or software are not keeping most of the algorithms used in bioinformatics for Pairwise pace with the speed of data generation. Old Bioinformatics alignment, Multiple Alignment and Motif finding are not tools have very less performance, accuracy and scalability implemented for Hadoop or Spark. Scala is a powerful language while analyzing large amount of data. When storing, managing supported by Spark. It provides, constructs like traits, closures, and analyzing large amount of data which is being generated functions, pattern matching and extractors that make it suitable now a days, these tools require more time and cost with less for Bioinformatics applications. -
MATLAB Software for Extracting Protein Name and Sequence Information from FASTA Formatted Proteome File
MATLAB software for extracting protein name and sequence information from FASTA formatted proteome file Wenfa Ng Unaffiliated researcher, Singapore, Email: [email protected] Abstract FASTA file format is a common file type for distributing proteome information, especially those obtained from Uniprot. While MATLAB could automatically read fasta files using the built-in function, fastaread, important information such as protein name and organism name remain enmeshed in a character array. Hence, difficulty exists in automatic extraction of protein names from fasta proteome file to help in building a database with fields comprising protein name and its amino acid sequence. The objective of this work was in developing a MATLAB software that could automatically extract protein name and amino acid sequence information from fasta proteome file and assign them to a new database that comprises fields such as protein name, amino acid sequence, number of amino acid residues, molecular weight of protein and nucleotide sequence of protein. Information on number of amino acid residues came from the use of the length built-in function in MATLAB analyzing the length of the amino acid sequence of a protein. The final two fields were provided by MATLAB built-in functions molweight and aa2nt, respectively. Molecular weight of proteins is useful for a variety of applications while nucleotide sequence is essential for gene synthesis applications in molecular cloning. Finally, the MATLAB software is also equipped with an error check function to help detect letters in the amino acid sequence that are not part of the family of 20 natural amino acids. Sequences with such letters would constitute as error inputs to molweight and aa2nt, and would not be processed.