Fundamentals of Bioinformatics - Ogurtsov A.N. 2013

List of Abbreviations

ASCII American Standard Code for Information Interchange defines 128 characters assigned to numbers 0-127.

BAC Bacterial Artificial Chromosome.

BIOS Basic Input-Output System.

BLAST Basic Local Structure/25.html">Alignment search Tool.

BLOSUM BLOcks SUbstitution Matrix - a substitution matrix used for scoring alignments between protein sequences.

BSML Bioinformatic Sequence Markup Language.

CERN From French Conseil Européen pour la Recherche Nucléaire - European Organization for Nuclear Research http://public.web.cern.ch/public/

CORBA Common Object Request Broker Architecture.

dbEST Database of Expressed Sequence Tags http://www.ncbi.nlm.nih.gov/nucest

DBMS Database Management System.

DDBJ DNA DataBank of Japan http://www.ddbj.nig.ac.jp/

EMBL European Molecular Biology Laboratory: http://www.embl.de/

EST Expressed Sequence Tags.

ExPASy Expert Protein Analysis System - the first molecular biology web server http://www.expasy.org

FASTA Fast Alignment.

FASTP FASTP algorithm.

FDA Food and Drug Administration.

FISH Fluorescence In Situ Hybridization - a cytogenetic technique used to detect and localize specific DNA sequences on Chromosomes.

FTP File Transfer Protocol.

GI GenInfo Identifiers - accession numbers for Biological Sequences submitted to NCBI Entrez.

HGP Human Genome Project.

HMM Hidden Markov Model.

HTML HyperText Markup Language.

HTTP Hypertext Transfer Protocol.

HUGE HUman Genome Equivalents - the Amount of Information contained in The Human Genome.

IDL Interface Definition Language - Interface Definition Language.

NBRF National Biomedical Research Foundation - National Biomedical Research Foundation.

NCBI National Center for Biotechnology Information - National Center for Biotechnology Information.

NHGRI National Human Genome Research Institute — National Human Genome Research Institute.

NIH National Institute of Health - National Institutes of Health: http://www.nih.gov/

NLM National Library of Medicine — National Library of Medicine.

ORF Open Reading Frame - Open Reading Frame.

PAGE Polyacrylamide gel Electrophoresis - Polyacrylamide Gel Electrophoresis.

PAM Percent Accepted Mutation - Percent Accepted Mutation.

PCR Polymerase Chain Reaction - Polymerase Chain Reaction.

PDB Protein data bank - Protein Data Bank: http://www.pdb.org/

PERL Practical Extraction and Reporting Language - Practical Extraction and Reporting Language.

PFGE Pulsed Field Gel Electrophoresis - Pulsed Field

Gel Electrophoresis. A method for separating large (up to 10 MBр) DNA fragments.

PHI-BLAST Pattern Hit Initiated BLAST - Pattern Hit Initiated BLAST.

PIR Protein Information Resource - Protein Information Resource: http://pir.georgetown.edu/

PRF Protein Research Foundation protein database (Osaka): http://www.genome.jp/dbget-bin/www_bfind?prf

PSI-BLAST Position-Specific Iterative BLAST - Position-Specific Iterative BLAST.

RFLP Restriction Fragment Length Polymorphism - Restriction Fragment Length Polymorphism.

SAGE Serial ANALYSIS OF Gene Expression - Serial Analysis of Gene Expression.

SDS-PAGE Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis -

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

SeqDB The Sequence Database - The Sequence Database:

http://pgrc-35.ipk- gatersleben.de/portal/page/portal/PG_BICGH/P_BICGH/P_BICGHRESOURCES/SeqDB

SGML Standard Generalized Markup Language - Standard Generalized Markup Language.

SNP Single Nucleotide Polymorphism

polymorphism or single nucleotide polymorphism is a DNA sequence variation of a single nucleotide.

SRS Sequence Retrieval System: http://srs.ebi.ас.uk/

STS Sequence Tagged Site.

Swiss-Prot Protein sequence database of the Swiss

Institute of Bioinformatics (Swiss Institute of Bioinformatics, http://www.isb-sib.ch/): http://www.expasy.org/sprot/

TCP Transmission Control Protocol.

TCP/IP Transmission Control Protocol / Internet Protocol.

URL Uniform Resource Locator.

UTR UnTranslated Region.

VNTR Variable Number of Tandem Repeat.

XML Extensible Markup Language.

YAC Yeast Artificial Chromosome.