Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00196 NAME GETREG DOMAIN RNA analysis DESCRIPTION The program getreg generates "single entry" sol files and a DESCRIPTION input data file for NEWTREE which will be used for structure DESCRIPTION comparison. DESCRIPTION The input file for the program is a region table file derived DESCRIPTION from lrna (suboptimal RNA folding program). AUTHOR Shu-Yun Le RA Le S.-Y, Zuker M.; RT "Predicting Common Foldings of Homologous RNAs."; RL J. Biomol. Struct. Dyn. 8:1027-1044(1991). RX Medline; 91345773. RX SeqAnalRef; LESY9102. RA Le S.-Y, Zuker M.; RT "Common Structures of the 5' Non-coding RNA in Enteroviruses and RT Rhinoviruses: Thermodynamical stability and statistical RT significance."; RL J. Mol. Biol. 216:729-741(1990). RX Medline; 91080160. RT Le S.-Y., Owens J., Nussinov R., Chen J.-H., Shapiro B., RT Maizel J.V. Jr.; RT "RNA Secondary Structures: Comparison and Determination of RT of Frequently Recurring Substructures by Consensus."; RL Comput. Appl. Biosci. 5:205-210(1989). RX Medline; 89353666. RX SeqAnalRef; LESY8901. ADDRESS Michael Zuker, PhD, ADDRESS Institute for Biomedical Computing, Box 8036 ADDRESS Washington University, 700 S. Euclid Ave. ADDRESS St. Louis, MO 63110, USA. ADDRESS Tel: +1 (314) 362-2932. Fax: +1 (314) 362-0234 CONTACT zuker@snark.wustl.edu SITE ftp anonymous snark.wustl.edu SITE Directory /pub SITE WWW Server at URL http://www.ibc.wustl.edu/~zuker SITE-CONTACT zuker@snark.wustl.edu OS - LANGUAGE - VOLUME - AC BC00197 NAME MFOLD DOMAIN RNA analysis DESCRIPTION Michael Zuker's Suboptimal RNA Folding package. DESCRIPTION A dynamic programming algorithm is used to DESCRIPTION find optimal and suboptimal foldings of an RNA DESCRIPTION molecule starting from linear sequence data. DESCRIPTION Auxiliary information can be used to constrain DESCRIPTION the folding AUTHOR Zuker M. and Jaeger J. RA Zuker M.; RT "Prediction of RNA Secondary Structure by Energy RT Minimization."; RL (In) Computer Analysis of Sequence Data RL A.M. Griffin and Griffin eds. RL Methods in Molecular Biology, Humana Press Inc., 267-294 (1994) RX SeqAnalRef; ZUKM9401. ADDRESS Michael Zuker, PhD, ADDRESS Institute for Biomedical Computing, Box 8036 ADDRESS Washington University, 700 S. Euclid Ave. ADDRESS St. Louis, MO 63110, USA. ADDRESS Tel: +1 (314) 362-2932. Fax: +1 (314) 362-0234 CONTACT zuker@snark.wustl.edu SITE ftp anonymous snark.wustl.edu SITE Directory /pub SITE WWW Server at URL http://www.ibc.wustl.edu/~zuker SITE-CONTACT zuker@snark.wustl.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/rnafold SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu SITE ftp anonymous frodo.mgh.harvard.edu SITE Directory /vax SITE-CONTACT Mike Cherry: cherry@frodo.mgh.harvard.edu OS Vax/VMS LANGUAGE - VOLUME - AC BC00198 NAME NAVIEW DOMAIN RNA analysis DESCRIPTION A group of programs and scripts that produce plots of RNA DESCRIPTION secondary structures DESCRIPTION naview - generates nucleic acid secondary structure information DESCRIPTION as an ASCII file containing device independent plot commands; DESCRIPTION genss - uses the NAVIEW output plus corresponding structural DESCRIPTION information to produce input suitable for the STRED (XRNA) DESCRIPTION program; DESCRIPTION plt2ps - uses the NAVIEW output and produces a modified radial DESCRIPTION drawing of the secondary structure, in PostScript form; DESCRIPTION auto_ct2ps - runs awk to split a multi-structure ct file into DESCRIPTION single structure files, then runs naview.exe and plt2ps.exe for DESCRIPTION each structure, without user input during execution; AUTHOR Robert E. Bruccoleri RA Bruccoleri R.E., Heinrich G.; RT "An improved algorithm for nucleic acid secondary structure RT display."; RL Comput. Appl. Biosci. 4:167-173(1988). RX Medline; 88252880. RX SeqAnalRef; BRUR8801. ADDRESS Cellular and Molecular Research Laboratory, ADDRESS Massachusetts General Hospital, Boston 02114, USA. CONTACT - SITE ftp anonymous nrcbsa.bio.nrc.ca SITE Directory /pub SITE-CONTACT zucker@nrcbsa.bio.nrc.ca OS UNIX LANGUAGE Bourne shell, Ansi C VOLUME - COMMENTS naview, genss and plt2ps are Bourne shell scripts that run COMMENTS executables naview.exe, genss.exe and plt2ps.exe respectively, COMMENTS as compiled from the ANSI C programming language source code. AC BC00199 NAME NEWTREE DOMAIN RNA analysis DESCRIPTION NewTree is used to do comparison of RNA secondary structures DESCRIPTION and is based on topological similarity searches. In the DESCRIPTION comparison, the optimal and suboptimal secondary structures of DESCRIPTION RNAs are represented by ordered labelled trees or forests. DESCRIPTION Only one type of structural elements of RNA secondary structure, DESCRIPTION the helix, is denoted by a node of the tree. The type and size DESCRIPTION of the loop (bulge and interior loops in the structure can be DESCRIPTION determined by the data stored in these two nodes. A leaf node DESCRIPTION defines a hairpin loop and a parent and its two or more sons DESCRIPTION define a multistem or multibranched structure. AUTHOR Shu-Yun Le RA Le S.-Y, Zuker M.; RT "Predicting Common Foldings of Homologous RNAs."; RL J. Biomol. Struct. Dyn. 8:1027-1044(1991). RX Medline; 91345773. RX SeqAnalRef; LESY9102. RA Le S.-Y, Zuker M.; RT "Common Structures of the 5' Non-coding RNA in Enteroviruses and RT Rhinoviruses: Thermodynamical stability and statistical RT significance."; RL J. Mol. Biol. 216:729-741(1990). RX Medline; 91080160. RT Le S.-Y., Owens J., Nussinov R., Chen J.-H., Shapiro B., RT Maizel J.V. Jr.; RT "RNA Secondary Structures: Comparison and Determination of RT of Frequently Recurring Substructures by Consensus."; RL Comput. Appl. Biosci. 5:205-210(1989). RX Medline; 89353666. RX SeqAnalRef; LESY8901. ADDRESS Michael Zuker, PhD, ADDRESS Institute for Biomedical Computing, Box 8036 ADDRESS Washington University, 700 S. Euclid Ave. ADDRESS St. Louis, MO 63110, USA. ADDRESS Tel: +1 (314) 362-2932. Fax: +1 (314) 362-0234 CONTACT zuker@snark.wustl.edu SITE ftp anonymous snark.wustl.edu SITE Directory /pub SITE WWW Server at URL http://www.ibc.wustl.edu/~zuker SITE-CONTACT zucker@snark.wustl.edu OS IRIS Version LANGUAGE - VOLUME - AC BC00200 NAME Vienna RNA Package DOMAIN RNA analysis DESCRIPTION Tools for prediction and comparison of RNA secondary structures. DESCRIPTION The Vienna RNA package consists of several stand-alone DESCRIPTION programs and a code library to link your own programs with. DESCRIPTION Secondary structure prediction by dynamic programming is used DESCRIPTION to obtain optimal structures (Zuker & Stiegler 1981) as well DESCRIPTION as base-pair probabilities (McCaskill 1990). DESCRIPTION Secondary structures can be compared using tree-editing or DESCRIPTION string alignment with various cost functions. DESCRIPTION In addition we provide programs to calulate the specific heat DESCRIPTION and design sequences for a given structure (inverse folding). AUTHOR Ivo Hofacker RA Hofacker I., Fontana W., Stadler P., Schuster P.; RT "Fast Folding and Comparison of RNA Secondary Structures."; RL Monatshefte f. Chemie 125:167-188(1994) ADDRESS Institute fuer Theoretische Chemie ADDRESS Waehringerstr. 17 ADDRESS 1090 Wien, Austria CONTACT Ivo.Hofacker@tbi.univie.ac.at SITE WWW Server at URL http://www.tbi.univie.ac.at/~ivo/RNA/ SITE ftp anonymous ftp.itc.univie.ac.at SITE Directory /pub/RNA OS UNIX LANGUAGE C VOLUME - AC BC00378 NAME Rnadraw DOMAIN RNA analysis DESCRIPTION Rnadraw offers RNA optimal structure / DESCRIPTION basepair-probability matrix / heat curve calculation on Intel x86 DESCRIPTION compatible computers, providing a consistent user interface DESCRIPTION with many possibilities to view, print, import/export and edit DESCRIPTION calculation results. AUTHOR Ole Matzura RT - ADDRESS - CONTACT ole@mango.mef.ki.se SITE ftp anonymous broccoli.mfn.ki.se SITE Directory /pub/rnadraw SITE-CONTACT - SITE WWW Server at URL http://mango.mef.ki.se/~ole/rnadraw/rnadraw.html OS Intel x86 (or compatible) computer (386, 486, P5, P6 ),Windows 95, OS Windows NT or Window 3.1/3.11 with Win32s version 1.2 LANGUAGE - VOLUME 500Kb REQUIRES at least 8Mb of RAM COMMENTS Win32s is a subset of the Win32 API for Windows 3.1/3.11 available COMMENTS free from Microsoft. Memory requirements COMMENTS depend on sequence length and calculation type: COMMENTS COMMENTS seq. size calc. structure calc. matrix COMMENTS --------------------------------------------------- COMMENTS 250 390 Kb 650 Kb COMMENTS 500 1530 Kb 2540 Kb COMMENTS 750 3410 Kb 5690 Kb COMMENTS 1000 6100 Kb 10100 Kb COMMENTS 1250 9440 Kb 15730 Kb COMMENTS 1500 13570 Kb 22620 Kb AC BC00389 NAME RNA_d2 DOMAIN RNA analysis DESCRIPTION RNA_d2 is a user-friendly program developped for interactively DESCRIPTION generating aesthetic and non-overlapping drawings of RNA DESCRIPTION secondary structures. It allows easy untangling and editing DESCRIPTION of RNA molecules > 1000 nucleotides long. AUTHOR J. Perochon-Dorisse, F. Chetouani, S. Aurel, N. Iscolo, AUTHOR B. Michot; RA Perochon-Dorisse J., Chetouani F., Aurel S., Iscolo N., RA Michot B.; RT "RNA_d2 : a computer program for editing and display RT of RNA secondary structures."; RL Comput. Appl. Biosci. 11:101-109(1995). RX Medline; 95316684. RX SeqAnalRef; PERJ9501. ADDRESS Institut de Biologie Cellulaire et Genetique du CNRS ADDRESS Laboratoire de Biologie Moleculaire Eucaryote du CNRS ADDRESS 118 route de Narbonnem 31062 Toulouse Cedex, France ADDRESS S.Aurel : ADDRESS Station de Biometrie et intelligence Artificielle, INRA, ADDRESS Chemin de Borde-Rouge,BP 27, 31326 Castanet Tolosan Cedex, France CONTACT rnad2@ibcg.biotoul.fr SITE ftp anonymous hpsrv.biotoul.fr SITE Directory /rna SITE-CONTACT - OS MS-DOS (386 PC or higher with a color screen, EGA or higher ) LANGUAGE C VOLUME - REQUIRES - COMMENTS The program is also available from the authors. COMMENTS Please send a 3.5in. floppy disk. AC BC00426 NAME SAMSON DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN Protein structure analysis DESCRIPTION The SAMSON package is a tool for advanced analysis of DESCRIPTION primary DNA, RNA and protein structures. The package consists DESCRIPTION of 16 programs performing statistical analysis and comparison DESCRIPTION of biopolymer sequences, search for homologies, translation of DESCRIPTION DNA and RNA sequences into amino acid sequences, splicing of DESCRIPTION RNA sequences and restriction map construction, recognition of DESCRIPTION functionally related sites in biopolymer molecules, textual DESCRIPTION analysis of DNA and RNA regulatory sites and prediction of DESCRIPTION intermolecular hybridization sites in DNA and RNA molecules. DESCRIPTION The SAMSON package consists of: DESCRIPTION - 16 applied programs in form of executable modules under DESCRIPTION MS-DOS v. 3.0 or higher; DESCRIPTION - the Microsoft FORTRAN 5.0 source library containing DESCRIPTION standard input-output and simple sequence processing routines; DESCRIPTION - ASCII-files with manuals (in russian); DESCRIPTION - helpfiles and other things that are need for learning DESCRIPTION the software usage. AUTHOR Nazipova N.N., Shabalina S.A., Ogurtsov A.Yu., Kondrashov A.S., AUTHOR Roytberg M.A., Butryakov G.V., Vernoslov S.E.; RA Nazipova N.N., Shabalina S.A., Ogurtsov A.Yu., RA Kondrashov A.S., Roytberg M.A., Butryakov G.V., RA Vernoslov S.E.; RT "SAMSON: a software package for the biopolymer RT primary structure analysis."; RL Comput. Appl. Biosci. 11(4):423-426 (1995). ADDRESS Institute of Mathematical Problems of Biology, ADDRESS Russian Academy of Sciences, Pushchino, Moscow region,142292 Russia CONTACT NNN@impb.serpukhov.su or shab@imbp.serpukhov.su SITE - SITE-CONTACT - OS MS-DOS LANGUAGE MS FORTRAN 5.0 VOLUME - REQUIRES MS-DOS v. 3.0 or higher AC BC00470 NAME Primer Premier 4 DOMAIN Oligomer design and synthesis DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN RNA analysis DOMAIN Restriction maps DESCRIPTION Primer Design Software DESCRIPTION Primer Premier 4 is now available for Power Macintosh and DESCRIPTION Window 3.1, NT as well as Windows 95. Primers can be DESCRIPTION designed for PCR, sequencing or hybridization probes DESCRIPTION automatically or with full manual control. DESCRIPTION From the selected pool of primers mutually compatible DESCRIPTION Nested/Multiplex primers or pairs can be chosen. DESCRIPTION Any primer can be mutated using the editing facility. DESCRIPTION Full degeneracy is supported. Comprehensive analyis of DESCRIPTION secondary structures as well as a table of properties DESCRIPTION including melting temperature calculated using nearest DESCRIPTION neighbor theory and optimal annealing temperature is DESCRIPTION displayed for each primer. DESCRIPTION DESCRIPTION The selected primers can be managed with the database DESCRIPTION storage facility. The program even makes the primer DESCRIPTION synthesis process painless by automatically creating an DESCRIPTION order form addressed to the vendor of your choice. DESCRIPTION DESCRIPTION Restriction enzyme analysis is available with multiple DESCRIPTION output formats: table, annotated sequence or map. Functions DESCRIPTION to edit the sequence and to translate it using standard or DESCRIPTION any mitochondrial/organelle codon table is provided. Graphs DESCRIPTION of melting temperature, internal stability and free energy DESCRIPTION are available on-line as well as in printed format. AUTHOR Premier Biosoft International RT - ADDRESS 3786 Corina Way ADDRESS Palo Alto, CA 94303 CONTACT sales@PremierBiosoft.com SITE WWW Server at URL http://www.PremierBiosoft.com OS Windows 95, 98, NT, 3.1, Power Macintosh LANGUAGE - VOLUME - REQUIRES - COMMENTS Commercial product, fully functional demo available at COMMENTS http://www.PremierBiosoft.com page. AC BC00496 NAME RNABOB DOMAIN RNA analysis DOMAIN Searching databases DESCRIPTION The program "rnabob" searches for RNA motifs in sequence databases. DESCRIPTION Rather than searching simply for primary sequence matches, rnabob DESCRIPTION allows one to search for secondary and tertiary structural motifs as DESCRIPTION well. DESCRIPTION DESCRIPTION The underlying algorithm is a non-deterministic finite state machine DESCRIPTION very similar to that used by UNIX regular expression pattern matching DESCRIPTION algorithms, but with the modification that downstream nodes may be DESCRIPTION constructed dynamically based on matches at upstream nodes (thus, the DESCRIPTION ability to search for complementarity or other absolute covariances). AUTHOR Sean R. Eddy RA Gautheret D., Major F. and Cedergren R.; RT "Pattern searching/alignment with RNA primary and secondary RT structures: an effective descriptor for tRNA."; RL Comp. Apps. Biosci. 6:325-331 (1990). RA Eddy S.R.; RT "RNABOB: a program to search for RNA secondary structure motifs in RT sequence databases."; RL Unpublished. ADDRESS Dept. of Genetics ADDRESS Washington University School of Medicine ADDRESS 660 S. Euclid Box 8232 ADDRESS St. Louis MO 63110, USA CONTACT eddy@genetics.wustl.edu SITE ftp anonymous genome.wustl.edu SITE Directory /pub/eddy/ SITE-CONTACT - OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00527 NAME tRNAscan-SE DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN WWW server DOMAIN Statistical significance SERVER http://genome.wustl.edu/eddy/tRNAscan-SE/ DESCRIPTION tRNAscan-SE identifies transfer RNA genes in genomic DNA or DESCRIPTION RNA sequences. It combines the specificity of the Cove DESCRIPTION probabilistic RNA prediction package (Eddy & Durbin, 1994) DESCRIPTION with the speed and sensitivity of tRNAscan 1.3 (Fichant & DESCRIPTION Burks, 1991) plus an implementation of an algorithm described DESCRIPTION by Pavesi and colleagues (1994) which searches for DESCRIPTION eukaryotic pol III tRNA promoters. tRNAscan-SE identifies DESCRIPTION 99-100% of transfer RNA genes in DNA sequence while giving DESCRIPTION less than one false positive per 15 gigabases. The program DESCRIPTION searches at approximately 30,000 bp per second. Other DESCRIPTION features include prediction of tRNA secondary structure, DESCRIPTION and detection of unusual tRNA homologues such as DESCRIPTION selenocysteine tRNAs, tRNA-derived repetitive elements and DESCRIPTION tRNA pseudogenes. AUTHOR Todd M. Lowe, Sean R. Eddy RA Lowe T.M., Eddy S.R.; RT "tRNAscan-SE: a program for improved detection RT of transfer RNA genes in genomic sequence."; RL Nucleic Acids Res 25: 955-964 (1997). RA Eddy, S.R., Durbin, R.; RT "RNA Sequence Analysis Using Covariance Models"; RL Nucleic Acids Res. 22: 2079-2088 (1994). RA Fichant G.A., Burks C.; RT "Identifying potential tRNA genes in genomic RT DNA sequences"; RL J Mol Biol 220: 659-671 (1991). RA Pavesi A., Conterio F., Bolchi A., Dieci G., RA Ottonello S.; RT "Identification of new eukaryotic tRNA genes in RT genomic databases by a multistep weight matrix RT analysis of transcriptional control regions."; RL Nucleic Acids Res. 22:1247-1256 (1994). ADDRESS Dept. of Genetics ADDRESS Washington University School of Medicine ADDRESS 660 S. Euclid, Box 8232 ADDRESS St. Louis MO 63110 CONTACT lowe@genetics.wustl.edu SITE WWW Server at URL http://genome.wustl.edu/eddy/tRNAscan-SE/ OS UNIX LANGUAGE C, Perl VOLUME - REQUIRES Perl 5.0+ AC BC00539 NAME FAStRNA DOMAIN WWW server DOMAIN RNA analysis DOMAIN Searching databases SERVER http://www-igm.univ-mlv.fr/~mabrouk DESCRIPTION The FAStRNA program was defined to identify tRNA genes in DESCRIPTION complete genome sequences using a pattern matching approach. DESCRIPTION FAStRNA was tested on the yeast genome: less than 3 minutes DESCRIPTION were needed to scan both strands and results matched the DESCRIPTION annotations. AUTHOR Nadia El Mabrouk, Frederique Lisacek RA El Mabrouk N., Lisacek F. RT "Very fast identification of RNA lotifs in genomic DNA. RT Application to tRNA search in the yeast genome." RL J.Mol.Biol.264:46-55 (1996). ADDRESS N.El Mabrouk ADDRESS Institut G. Monge ADDRESS Universite de Marne-la-Vallee ADDRESS 93166 Noisy le Grand cedex, France ADDRESS F.Lisacek ADDRESS Laboratoire Genome et Informatique ADDRESS Universite de Versailles-Saint-Quentin ADDRESS 45 avenue des Etats-Unis ADDRESS 78035 Versailles cedex, France CONTACT mabrouk@monge.univ-mlv.fr CONTACT lisacek@genetique.uvsq.fr SITE WWW Server at URL http://www-igm.univ-mlv.fr/~mabrouk OS unix LANGUAGE C VOLUME - REQUIRES - AC BC00552 NAME ESSA DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN WWW server DESCRIPTION With ESSA, we propose an approach of RNA secondary DESCRIPTION structure analysis based on extensive viewing within a DESCRIPTION friendly graphical interface. This computer program is DESCRIPTION organized around the display of folding models produced by DESCRIPTION two complementary methods suitable to draw long RNA DESCRIPTION molecules. Any feature of interest can be managed directly DESCRIPTION on the display and highlighted by a rich combination of DESCRIPTION colours and symbols with emphasis given to structural probe DESCRIPTION accessibilities. ESSA also includes a word searching DESCRIPTION procedure allowing easy visual identification of structural DESCRIPTION features even complex and degenerated. Analysis functions DESCRIPTION make it possible to calculate the thermodynamic stability DESCRIPTION of any part of a folding using several models and compare DESCRIPTION homologous aligned RNA both in primary and secondary DESCRIPTION structure. The predictive capacities of ESSA which brings DESCRIPTION together the experimental, thermodynamic and comparative DESCRIPTION methods, are increased by coupling it with a program DESCRIPTION dedicated to RNA folding prediction based on constraints DESCRIPTION management AUTHOR Chetouani F., Monestie P., Thebault P., Gaspin C., Michot B. RA Chetouani F., Monestie P., Thebault P., Gaspin C., Michot B.; RT "ESSA: An integrated and interactive computer tool for RT analysing RNA secondary structure."; RL Nucleic Acids Res 25(17):3514-3522(1997). ADDRESS Gaspin : Station de Biometrie et d'Intelligence Artificielle, ADDRESS I.N.R.A., Chemin de Borde-Rouge, Auzeville BP 27, 31326 ADDRESS Castanet-Tolosan Cedex, FRANCE ADDRESS tel : (33) 05 61 28 52 82; fax : (33) 05 61 28 53 35; ADDRESS e-mail : gaspin@toulouse.inra.fr ADDRESS Michot, Chetouani ADDRESS Laboratoire de Biologie Moleculaire Eucaryote du C.N.R.S., ADDRESS Universite Paul Sabatier, 118 route de Narbonne, ADDRESS 31062 Toulouse Cedex, FRANCE ADDRESS tel : (33) 05 61 33 58 65; fax : (33) 05 61 33 58 86; ADDRESS e-mail : bmichot@ibcg.biotoul.fr farid@ibcg.biotoul.fr CONTACT essa@toulouse.inra.fr SITE WWW Server at URL http://www-bia.inra.fr/T/essa/Doc/essa_home.html OS UNIX : SUN, SGI, HP LANGUAGE C VOLUME 200 Kb REQUIRES - AC BC00587 NAME BioEdit DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Searching databases DOMAIN General tools DESCRIPTION BioEdit is a user-friendly, graphically-oriented sequence DESCRIPTION alignment editor for Windows 95/98/NT. Features include DESCRIPTION several modes of hand alignment, auto-linking to ClustalW, DESCRIPTION user-defined color view (editable by mouse point- and DESCRIPTION click), separate amino acid and nucleotide color tables, DESCRIPTION Shaded views with many options, RNA comparative analysis DESCRIPTION tools (including mutual information with interactive 2-D DESCRIPTION matrix plots and area plots), restriction mapping, browsing DESCRIPTION restriction enzymes by company, easy plasmid drawing and DESCRIPTION annotation, protein hydropathy plots, can handle very large DESCRIPTION alignments (up to 20000 sequences of undefined length), DESCRIPTION several translation modes, nucleotide/translation toggling DESCRIPTION for alignment in both protein and DNA views, 6-frame DESCRIPTION translations, basic sequence manipulations (complement, DESCRIPTION reverse, uppercase, lowercase), internal web browser (HTML DESCRIPTION 2.0-compliant), auto-link to external browser with internet DESCRIPTION bookmarks, on-line help system, configure external apps via DESCRIPTION a graphical interface to automatically run through a DESCRIPTION BioEdit interface, split-window views for editing of two DESCRIPTION different places in an alignment at the same time, local DESCRIPTION NCBI BLAST accessories, single sequence editing and DESCRIPTION manipulation, retains GenBank data (eg, FEATURES, DESCRIPTION REFERENCE, SOURCE, PID or NID, etc), binary file format for DESCRIPTION fast save/open of very large files (alignments up to 100 Mb DESCRIPTION and more are no problem), correct spacing of all available DESCRIPTION fonts in edit window and in shaded view, creation of DESCRIPTION high-quality alignment figures via shading with many DESCRIPTION options (including full-color, id/sim shading, enhanced DESCRIPTION metafile copy and paste directly into graphics programs), DESCRIPTION easy formatted text print preview. AUTHOR Tom Hall RT - ADDRESS Department of Microbiology, ADDRESS North Carolina State University ADDRESS Raleigh, NC 27695 CONTACT tahall2@unity.ncsu.edu SITE WWW Server at URL http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html OS Windows LANGUAGE - VOLUME BioEdit.zip file = 7.6 Mb REQUIRES Windows 95, 98 or NT, Pentium 60+, 16 Mb RAM+, REQUIRES 20 Mb hard drive space