Bioinformatics Methods and Protocols Edited by Stephen Misener Stephen A. Krawetz Methods in Molecular Biology Methods in Molecular Biology TM TM VOLUME 132 HUMANA PRESS HUMANA PRESS Bioinformatics Methods and Protocols Edited by Stephen Misener Stephen A. Krawetz Bioinformatics Methods and Protocols Edited by Stephen Misener Queen 'S University, Kingston, Ontario, Canada and Stephen A. Krawetz Wayne State University, Detroit, MI Humana Press $& Totowa, New Jersey [...]... enzymes, and reagents, protein analysis data files, transcription factor database (TFD), codon frequency tables, translation tables, and the PROSITE dictionary of protein sites and patterns Those data are stored in text files that individuals may retrieve and edit for customization and special purposes 3.3 Interfaces Two interfaces are included with the Wisconsin Package: the command-line interface and. .. familiar with the Wisconsin Package A discussion about the GCG programs themselves is included in Chapter 1 From: Methods in Molecular Biology, vol 132: Bioinformatics Methods and Protocols Edited by: S Misener and S A Krawetz © Humana Press Inc., Totowa, NJ 23 24 Womble 2 Materials The methods reported here are for the GCG program package version 9.1, installed on a shared computer with a UNIX operating... possible way to set up X-Windows and Seqlab, but they are generic and should be applicable in most situations Start the X-Windows server program on the PC and leave it running in the background Follow the instructions in the first part of the command line tutorial (Subheading 3.4.2.) to use telnet to connect to and login to the GCG server, change into the gcg folder, and startup the GCG programs The... login with the pre-assigned userid and password The UNIX command prompt will appear, looking something like this: UNIX% Commands are typed at the prompt Use UNIX commands to create a folder to contain the GCG working files by typing: UNIX% mkdir gcg and pressing the return key (type only the part after gcg directory by typing: UNIX%) Change into the UNIX% cd gcg and pressing the return key Startup... phylogenetic trees using distance methods, and calculate the degree of divergence of two protein-coding regions Gene finding and pattern recognition These programs help in recognition of coding regions, terminators, repeats, and consensus patterns Several of the programs help to analyze sequence composition Mapping These programs calculate and display restriction maps and peptide cleavage patterns Primer... connecting to and controlling the GCG server) and an X-Windows server program (for displaying X-Windows graphics and the SeqLab windows on the PC screen) Additional helpful tools include a Web browser (for reading the online GCG manuals), an FTP client (for transferring files to and from the GCG server), a text editor, such as the Windows Notepad program (for editing text files on the PC), and printer... PepPlot, PeptideStructure, and so on) assist in determining information about protein amino acid sequences, such as plotting the isoelectric point, location of functional motifs, and predictions of various aspects of protein secondary structure, including antigenicity and secretory signals 3.1.11 RNA Secondary Structure Programs in this group (Mfold, StemLoop, and so on) can predict and display in multiple... return key Startup the GCG programs by typing: UNIX% gcg and pressing the return key The GCG welcome banner will scroll across the screen, listing the available databases, and, after a moment, the command prompt will return Use the GCG fetch command to bring back a copy of the DNA sequence of the M13mp18 cloning vector by typing: UNIX% fetch m13mp18 and pressing the return key A file named m13mp18.gb_sy... (ChopUp, Replace, Reformat, and so on) assist in manipulating text files, printing GCG documentation, and other tasks 3.2 Databases A comprehensive set of sequence databases is included with the Wisconsin Package These include the GenBank and EMBL nucleotide sequence databases (with the EMBL databases abridged to avoid duplication with sequences in GenBank), and the PIR and SwissProt protein sequence... Frames, Motifs, and so on), which assist in identifying protein-coding regions, proteinbinding motifs, direct repeats and other patterns, and other similar tasks 3.1.7 Importing / Exporting Fifteen programs in this group assist in entering sequence data and converting the data between the various sequence file formats, including formats for GCG, Staden, EMBL, GenBank, IntelliGenetics, PIR, and FASTA GCG . Bioinformatics Methods and Protocols Edited by Stephen Misener Stephen A. Krawetz Methods in Molecular Biology Methods in Molecular Biology TM TM VOLUME 132 HUMANA PRESS HUMANA PRESS Bioinformatics Methods. Biology TM TM VOLUME 132 HUMANA PRESS HUMANA PRESS Bioinformatics Methods and Protocols Edited by Stephen Misener Stephen A. Krawetz Bioinformatics Methods and Protocols Edited by Stephen Misener Queen 'S. Protocols Edited by Stephen Misener Queen 'S University, Kingston, Ontario, Canada and Stephen A. Krawetz Wayne State University, Detroit, MI Humana Press $& Totowa,