The Art of Multiple Sequence Alignment in R
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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 -
DECIPHER: Harnessing Local Sequence Context to Improve Protein Multiple Sequence Alignment Erik S
Wright BMC Bioinformatics (2015) 16:322 DOI 10.1186/s12859-015-0749-z RESEARCH ARTICLE Open Access DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment Erik S. Wright1,2 Abstract Background: Alignment of large and diverse sequence sets is a common task in biological investigations, yet there remains considerable room for improvement in alignment quality. Multiple sequence alignment programs tend to reach maximal accuracy when aligning only a few sequences, and then diminish steadily as more sequences are added. This drop in accuracy can be partly attributed to a build-up of error and ambiguity as more sequences are aligned. Most high-throughput sequence alignment algorithms do not use contextual information under the assumption that sites are independent. This study examines the extent to which local sequence context can be exploited to improve the quality of large multiple sequence alignments. Results: Two predictors based on local sequence context were assessed: (i) single sequence secondary structure predictions, and (ii) modulation of gap costs according to the surrounding residues. The results indicate that context-based predictors have appreciable information content that can be utilized to create more accurate alignments. Furthermore, local context becomes more informative as the number of sequences increases, enabling more accurate protein alignments of large empirical benchmarks. These discoveries became the basis for DECIPHER, a new context-aware program for sequence alignment, which outperformed other programs on largesequencesets. Conclusions: Predicting secondary structure based on local sequence context is an efficient means of breaking the independence assumption in alignment. Since secondary structure is more conserved than primary sequence, it can be leveraged to improve the alignment of distantly related proteins. -
Analysis the Structure of SAM and Cracking Password Base on Windows Operating System
International Journal of Future Computer and Communication, Vol. 5, No. 2, April 2016 Analysis the Structure of SAM and Cracking Password Base on Windows Operating System Jiang Du and Jiwei Li latest Windows 10, the registry contains information that Abstract—Cracking Windows account password is critical to Windows continually references during operation, such as the forensic analyst. The general methods of decipher password profiles for each user, the applications installed on the include clean the password, guess by social engineering, computer and the types of documents, property sheet settings mathematical analyzing, exhaustive attacking, dictionary attacking and rainbow tables algorithm. This paper provides the of folders and application icons, what hardware exists on the details about the Security Account Manager(SAM) database system, and the ports that are being used [3]. On disk, the and describes how to get the user information from SAM and Windows registry is not only a large file but a set of discrete cracks account password of Windows 10 that the latest files called hives. Each hive is a hierarchical tree which operating system of Microsoft. identified by a root key to provide access to all sub-keys in the tree up to 512 levels deep. Index Terms—SAM, decipher password, crack password, Windows 10. III. SECURITY ACCOUNT MANAGER (SAM) I. INTRODUCTION Security Account Manager (SAM) is a database used to In the process of computer forensic the analyst need to store user account information, including password, account enter the Windows operating system by cracking windows groups, access rights, and special privileges in Windows account password to collect evidence at times. -
Decipher Prostate Cancer Classifier
Lab Management Guidelines v2.0.2019 Decipher Prostate Cancer Classifier MOL.TS.294.A v2.0.2019 Procedures addressed The inclusion of any procedure code in this table does not imply that the code is under management or requires prior authorization. Refer to the specific Health Plan's procedure code list for management requirements. Procedures addressed by this Procedure codes guideline Decipher Prostate Cancer Classifier 81479 What are gene expression profiling tests for prostate cancer Definition Prostate cancer (PC) is the most common cancer and a leading cause of cancer- related deaths worldwide. It is considered a heterogeneous disease with highly variable prognosis.1 High-risk prostate cancer (PC) patients treated with radical prostatectomy (RP) undergo risk assessment to assess future disease prognosis and determine optimal treatment strategies. Post-RP pathology findings, such as disease stage, baseline Gleason score, time of biochemical recurrence (BCR) after RP, and PSA doubling- time, are considered strong predictors of disease-associated metastasis and mortality. Following RP, up to 50% of patients have pathology or clinical features that are considered at high risk of recurrence and these patients usually undergo post-RP treatments, including adjuvant or salvage therapy or radiation therapy, which can have serious risks and complications. According to clinical practice guideline recommendations, high risk patients should undergo 6 to 8 weeks of radiation therapy (RT) following RP. However, approximately 90% of high-risk patients -
Comparing Tools for Non-Coding RNA Multiple Sequence Alignment Based On
Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press ES Wright 1 1 TITLE 2 RNAconTest: Comparing tools for non-coding RNA multiple sequence alignment based on 3 structural consistency 4 Running title: RNAconTest: benchmarking comparative RNA programs 5 Author: Erik S. Wright1,* 6 1 Department of Biomedical Informatics, University of Pittsburgh (Pittsburgh, PA) 7 * Corresponding author: Erik S. Wright ([email protected]) 8 Keywords: Multiple sequence alignment, Secondary structure prediction, Benchmark, non- 9 coding RNA, Consensus secondary structure 10 Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press ES Wright 2 11 ABSTRACT 12 The importance of non-coding RNA sequences has become increasingly clear over the past 13 decade. New RNA families are often detected and analyzed using comparative methods based on 14 multiple sequence alignments. Accordingly, a number of programs have been developed for 15 aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for 16 these tasks remain unclear because existing benchmarks contain too few sequences belonging to 17 only a small number of RNA families. RNAconTest (RNA consistency test) is a new 18 benchmarking approach relying on the observation that secondary structure is often conserved 19 across highly divergent RNA sequences from the same family. RNAconTest scores multiple 20 sequence alignments based on the level of consistency among known secondary structures 21 belonging to reference sequences in their output alignment. Similarly, consensus secondary 22 structure predictions are scored according to their agreement with one or more known structures 23 in a family. -
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. -
Getting Started Deciphering
Getting Started DECIPHERing Erik S. Wright May 19, 2021 Contents 1 About DECIPHER 1 2 Design Philosophy 2 2.1 Curators Protect the Originals . 2 2.2 Don't Reinvent the Wheel . 2 2.3 That Which is the Most Difficult, Make Fastest . 2 2.4 Stay Organized . 2 3 Functionality 3 4 Installation 5 4.1 Typical Installation (recommended) . 5 4.2 Manual Installation . 5 4.2.1 All platforms . 5 4.2.2 MacOSX........................................... 6 4.2.3 Linux ............................................. 6 4.2.4 Windows ........................................... 6 5 Example Workflow 6 6 Session Information 11 1 About DECIPHER DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R statistical programming language. The program features tools falling into five categories: Sequence databases: import, maintain, view, and export a massive number of sequences. Sequence alignment: accurately align thousands of DNA, RNA, or amino acid sequences. Quickly find and align the syntenic regions of multiple genomes. Oligo design: test oligos in silico, or create new primer and probe sequences optimized for a variety of objectives. Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes. Analyze sequences: find chimeras, classify into a taxonomy of organisms or functions, detect repeats, predict secondary structure, create phylogenetic trees, and reconstruct ancestral states. 1 Gene finding: predict coding and non-coding genes in a genome, extract them from the genome, and export them to a file. DECIPHER is available under the terms of the GNU Public License version 3. 2 Design Philosophy 2.1 Curators Protect the Originals One of the core principles of DECIPHER is the idea of the non-destructive workflow. -
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. -
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.