Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00154 NAME DegenDesigner DOMAIN Oligomer design and synthesis DESCRIPTION DegenDesigner (DD) is a program which aids in the selection of DESCRIPTION degenerate oligonucleotide sequences from a given peptide DESCRIPTION sequence. DegenDesigner Will allow the user to: DESCRIPTION 1. Backtranslate a peptide sequence to its corresponding DESCRIPTION nucleotide coding sequence. DESCRIPTION 2. View all potential forward and reverse primers (within a DESCRIPTION user-specified length range) that do not exceed a user-selected DESCRIPTION degeneracy limit (up to a maximum of 256 fold). For each primer DESCRIPTION DD will display the primer length, start position, degeneracy, DESCRIPTION and the range of melting temperatures. DESCRIPTION 3. Select a desired degenerate primer pair for use in PCR from a DESCRIPTION list of recommendations provided by DD. The recommendation DESCRIPTION feature is based on user-selected criteria. DESCRIPTION 4. Calculate the percentage of primers in the forward and reverse DESCRIPTION primer pools that form stable intramolecular or intermolecular DESCRIPTION secondary structures. AUTHOR Ramin Homayouni , Zhong Chen RT - ADDRESS Univ. of Houston, Dept. of Biochemistry ADDRESS 3201 Cullen, Rm 402 HSC Houston, TX 77204-5934, USA CONTACT Ramin Homayouni Ramin@dna.bchs.uh.edu SITE ftp anonymous evolution.bchs.uh.edu SITE Directory /pub/gene-server/unix SITE-CONTACT - OS NeXTs running Nextstep 3.0. LANGUAGE - VOLUME - AC BC00155 NAME OSP DOMAIN Oligomer design and synthesis DESCRIPTION OSP is a computer program developed to aid in DESCRIPTION selecting oligonucleotide primers for DNA DESCRIPTION sequencing and for the polymerase chain DESCRIPTION reaction. OSP allows the user to specify (or DESCRIPTION use default) constraints for primer and DESCRIPTION amplified product lengths, %G+C contents, DESCRIPTION and (absolute or relative) meltingtemperatures DESCRIPTION for primer 3' nucleotides; and for the maximum DESCRIPTION allowable primer-self,primer-primer, and DESCRIPTION primer-product annealing propensities. DESCRIPTION Candidate primer sequences are screened DESCRIPTION against a user-supplied data set of other DESCRIPTION sequences (e.g. repetitive element or vector DESCRIPTION sequences) to help minimize the possibility of DESCRIPTION non-specific priming. DESCRIPTION Primers meeting all constraints are ranked and DESCRIPTION displayed in order of increasing overall DESCRIPTION ``score'', which is a user-definable weighted DESCRIPTION sum of the above parameter values. DESCRIPTION The program is available at no cost from the DESCRIPTION authors in two versions, one of which produces DESCRIPTION text-only output, and the other having an DESCRIPTION interactive X windows graphic interface. AUTHOR LaDeana Hillier RA Hillier L, Green P.; RT "OSP: A computer program for choosing PCR RT and DNA sequencing primers."; RL PCR Methods and Applications 1:124-128(1991). RX Medline; 93113324. RX SeqAnalRef; HILL9101. ADDRESS Washington University Medical School ADDRESS Department of Genetics, Box 8232, 4566 Scott, ADDRESS St. Louis, MO 63110 USA. CONTACT LaDeana Hillier lfw@elegans.wustl.edu SITE - SITE-CONTACT - OS VAX/VMS, PC, MAC, and SUN Sparcstations), OS or interactive X windows graphics version OS (X-Window version for the Sparc and now for Linux). LANGUAGE C VOLUME - AC BC00156 NAME PCAP DOMAIN Oligomer design and synthesis DESCRIPTION Probe Choice & Analysis Package DESCRIPTION PCAP is a suite of programs that: (i) convert Genbank files in DESCRIPTION to a format useable by the package; (ii) calculate trinucleotide DESCRIPTION and tetranucleotide frquencies in available genomic sequence on DESCRIPTION a particular species: (iii) present the user with upper and lower DESCRIPTION bounds on the frequencies of hybridization sites for DESCRIPTION oligonucleotide probes of length 8-12; (iv) allow the user to DESCRIPTION place constraints on site frequency and G+C content of probes DESCRIPTION and provides a list of short probe sequences that fit these DESCRIPTION criteria. Predictions of a hybridization site's frequency of DESCRIPTION occurrence is based on fitting a third-order Markov chain model DESCRIPTION to the genomic sequence data presented to the program. AUTHOR A. Jamie Cuticchia RA Cuticchia A.J., Arnold J., Timberlake W.E.; RT "PCAP: probe choice and analysis package - set of programs to RT aid in choosing synthetic oligomers for contig mapping."; RL Comput. Appl. Biosci. 9:201-203(1993). RX Medline; 93245050. RX SeqAnalRef; CUTA9301. ADDRESS - CONTACT - SITE The software is only distributed via Internet using EMAIL. SITE Please send an EMAIL request to: ARNOLD@BSCF.UGA.EDU SITE-CONTACT - OS VMS screen management utilities under VT100 terminal emulation. LANGUAGE FORTRAN-77 VOLUME - AC BC00157 NAME PRIMEGEN DOMAIN Oligomer design and synthesis DESCRIPTION Primegen is a multiple alignment analysis tool DESCRIPTION for finding the least-degenerate, most- DESCRIPTION degenerate, least-conserved, and most- DESCRIPTION conserved regions of protein and nucleic acid DESCRIPTION multiple alignments, and generating DESCRIPTION oligonucleotide primers for these regions. DESCRIPTION Primegen does not create multiple alignments, DESCRIPTION but only analyses alignments created DESCRIPTION elsewhere. AUTHOR Patrick J. O'Hara and Domenick Venezia RT - ADDRESS Scientific Computing Service CONTACT - SITE - SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00158 NAME PRIMER - MIT DOMAIN Oligomer design and synthesis DESCRIPTION PRIMER is a computer program for selecting PCR primer pairs to DESCRIPTION amplify specific regions of sequenced DNA. While PRIMER was DESCRIPTION specifically designed to select primers from cloned and DESCRIPTION sequenced genomic DNAs, many of the tests it performs are useful DESCRIPTION for selecting oligos for other types of experiments as well, DESCRIPTION including other PCR applications, oligo hybridization and DESCRIPTION dideoxy sequencing. DESCRIPTION There are two versions of this program : primer.0.5 and Primer2.2 AUTHOR Stein L., Daly M. and Lander E. RT - ADDRESS MIT Center for Genome Research ADDRESS Whitehead Institute for Biomedical Research ADDRESS Nine Cambridge Center, Cambridge, Massachusetts 02142,USA CONTACT primer@genome.wi.edu SITE ftp anonymous genome.wi.mit.edu SITE Directory /pub/primer.0.5 SITE-CONTACT rnahf@genome.wi.mit.edu SITE ftp anonymous genome.wi.mit.edu SITE Directory /pub/software/Primer2.2 SITE-CONTACT rnahf@genome.wi.mit.edu OS Unix workstations including Sun SPARCStation OS and DEC DECStation systems, Mac and PC for version 0.5 LANGUAGE C VOLUME - COMMENTS PRIMER is available for free use for non- COMMENTS commercial purposes by basic research labs in COMMENTS both academia and industry, providing users COMMENTS register using the form supplied with the COMMENTS program. AC BC00159 NAME PRIMER - Stanford DOMAIN Oligomer design and synthesis DESCRIPTION The program 'primer' helps to find potential DESCRIPTION mispriming sites (primer sequences should be DESCRIPTION designed before running the program!).The pro- DESCRIPTION gram allows to give higher weights to matches DESCRIPTION at the 3'end of the primer, linearly DESCRIPTION decreasing them towards the 5' end (the default DESCRIPTION is weight=10 for 3' nucleotide decreasing to 1 DESCRIPTION at nucleotide # 8 from the 3'end). The program DESCRIPTION can be used when amplifying *long* fragments DESCRIPTION from a known sequence. AUTHOR Don Faulkner RT - ADDRESS - CONTACT - SITE ftp anonymous jmullins.stanford.edu SITE Directory /pub SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/primer SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu OS Sun workstation (Unix). LANGUAGE C VOLUME - AC BC00262 NAME AMPLIFY DOMAIN Oligomer design and synthesis DESCRIPTION This Macintosh software is for use in designing, analyzing, and DESCRIPTION simulating experiments involving the polymerase chain reaction DESCRIPTION (PCR). PCR is a technique used by molecular biologists to DESCRIPTION amplify highly selected segments of DNA. If you never heard of DESCRIPTION PCR, you probably have no use for this program. To use Amplify DESCRIPTION you must supply the sequences of the primers and the target DNA. DESCRIPTION The software then analyzes the combination of primers and target DESCRIPTION sequence you have chosen to determine what portions of the DESCRIPTION target are likely to be amplified. The result is a graphical map DESCRIPTION of the target sequence, primer binding sites and amplified DESCRIPTION fragments. The program also provides various bits of helpful DESCRIPTION information about the reaction products, primer binding sites, DESCRIPTION potential dimer formation, etc., that can help in planning a PCR DESCRIPTION experiment and designing primers. AUTHOR Bill Engels RA Engels W.R.; RT "Contributing software to the Internet: the Amplify program."; RL Trends Biochem. Sci. 18:448-450(1993). RX Medline; 94120559. RX SeqAnalRef; ENGW9301. ADDRESS Genetics Department, University of Wisconsin, ADDRESS Madison, WI 53706, USA CONTACT WREngels@macc.wisc.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/mac SITE-CONTACT nethelp@ebi.ac.uk OS MacOS LANGUAGE VOLUME - AC BC00420 NAME PRIMER-MASTER DOMAIN Oligomer design and synthesis DESCRIPTION Automatical search and selection of optimal primers and primers DESCRIPTION pairs for various variants of PCR; Analysis of oligs supposed DESCRIPTION to be used as PCR primers or hybridization probes; Editor for DESCRIPTION comfortable typing-in new nucleotide sequences; AUTHOR Proutski Vitali, Sokur Oleg RA Proutski V.Y., Sokur O.V.; RT "New orginal software for optimized design of RT PCR primers."; RL (In) Abstracts of the IX International Conference RL "Progress in Clinical Virology",(August 1994, Stockholm). ADDRESS Institute of Influenza & Other Viral Infections of RAMS ADDRESS 197376 Prof.Popova str. 15/17, St.Petersburg, Russia CONTACT proutski@influenza.spb.su SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos SITE-CONTACT nethelp@ebi.ac.uk OS MS-DOS LANGUAGE Turbo C 2.0 VOLUME 222682 bytes REQUIRES Nothing particular, only IBM PC or compatible COMMENTS Files : primer.exe (contains executable primerm.exe) COMMENTS and primread.exe (contains the readme file) AC BC00427 NAME DataMinder DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Oligomer design and synthesis DOMAIN Database and analysis DESCRIPTION DataMinder is a standalone data management program designed DESCRIPTION for molecular biologists. One can readily store and retrieve DESCRIPTION data about oligonucleotides, nucleic acid or protein DESCRIPTION sequences, recombinant DNA clones, cells, reagents and DESCRIPTION protocols .A number of utilities for data analysis are provided, DESCRIPTION including those for calculating the Tms of oligonucleotides and DESCRIPTION for the evaluation of oligonucleotides for use as DESCRIPTION hybridization probes or primers for DNA synthesis. A DESCRIPTION variety of sequence editing features including voice veri- DESCRIPTION fication and the ability to import and export sequence data DESCRIPTION in a variety of different formats are also provided.Context- DESCRIPTION sensitive help is provided. DataMinder is simple to use and to DESCRIPTION customize and allows for sharing of database information DESCRIPTION across a computer network. AUTHOR Karen Usdin RA Usdin K.; RT "Hypercard-based data management tools for molecular biologists."; RL Comput. Appl. Biosci. 8:107-111(1992). RX Medline; 92274208. RX SeqAnalRef; USDK9201. ADDRESS Building 8, Room 202 ADDRESS 8 Center DR MSC 0830 ADDRESS National Institutes of Health ADDRESS Bethesda, MD 20892-0830 ADDRESS U.S.A. CONTACT ku@helix.nih.gov SITE - SITE-CONTACT - OS MAC LANGUAGE C, hypertalk VOLUME - REQUIRES Mac SE or above, 2MB Ram AC BC00429 NAME Primer Design DOMAIN Oligomer design and synthesis DESCRIPTION PrimerDesign is a DOS-program to choose primer for PCR or DESCRIPTION oligonucleotide probes. It is tailored to check known DESCRIPTION sequences for repeats and unique sequences and subsequencly DESCRIPTION to create prober primers according to this data. A lot of DESCRIPTION constrains are available to meet your conditions. It can DESCRIPTION handle up to 31500 base pairs. DESCRIPTION Additional features: Unique sequences, repeats, restriction sites AUTHOR Andreas Becker, Joerg Napiwotzki RA Napiwotzki J., Becker A., Damian M.; RT "Primer Design - a new program to choose PCR primers RT and oligonucleotide probes."; RL Medizinische Genetik, Programme and Abstracts, Vol. 2 (1995). AB This paper is available at the following AB URL http://www.chemie.uni-marburg.de/~becker/poster/poster4.html ADDRESS Andreas Becker ADDRESS Friedrich-Ebert-Strasse 36 ADDRESS 35039 Marburg, Germany CONTACT becker@ps1515.chemie.uni-marburg.de SITE ftp anonymous ftp.chemie.uni-marburg.de SITE Directory /pub/PrimerDesign SITE-CONTACT becker@ps1515.chemie.uni-marburg.de SITE WWW Server at URL http://www.chemie.uni-marburg.de/~becker/pdhome.html OS PC (DOS) LANGUAGE Basic VOLUME - REQUIRES - 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 BC00473 NAME Primers! for the Mac DOMAIN Oligomer design and synthesis DOMAIN Sequence analysis DESCRIPTION Primers! for the Mac is a shareware Macintosh application DESCRIPTION for picking primers for PCR and other applications. It DESCRIPTION allows the user to interactively scroll through all possible DESCRIPTION primers and primer pairs, to pick the optimal primer for DESCRIPTION his or her needs. AUTHOR Richard Resnick RT - ADDRESS - CONTACT rjr@applepi.com SITE ftp anonymous wuarchive.wustl.edu SITE Directory /systems/mac/info-mac/sci/primers-10-installer.hqx SITE-CONTACT - SITE WWW Server at URL http://www.applepi.com/macprimerinfo.html OS Macintosh LANGUAGE English VOLUME Approximately 300 KB REQUIRES Color Macintosh, System 7 or better, English Dialect AC BC00478 NAME Primer Premier 4 DOMAIN Oligomer design and synthesis DESCRIPTION Primer Premier 4 is part of the new generation of DESCRIPTION automatic primer selection programs. Using a DESCRIPTION sophisticated search engine, it finds the best primers in DESCRIPTION a sequence based on the latest algorithms automatically. DESCRIPTION Just load the sequence, click auto-search, and get the best DESCRIPTION primers in the sequence. It will even store the new DESCRIPTION primers in a database and print a synthesis form for easy DESCRIPTION ordering. DESCRIPTION DESCRIPTION Degenerate Primers DESCRIPTION Primer Premier facilitates design of degenerate primers. DESCRIPTION Degenerate sequences can be generated by reverse DESCRIPTION translation using the standard codon table or any of DESCRIPTION several mitochondrial codon tables. DESCRIPTION The reverse translated sequence is then searched for DESCRIPTION regions of low degeneracy and primers are selected. The DESCRIPTION user can set both the maximum number of amibigious bases DESCRIPTION within 6 of the 3' end of the primer and the maximum DESCRIPTION percent of degenerate bases within the primer. DESCRIPTION DESCRIPTION Nested/Multiplex Primers DESCRIPTION The nested/multiplex primer tool enabled the user to DESCRIPTION select pools of compatible primers for use in multiplex DESCRIPTION sequencing or nested PCR. By checking for cross-homology DESCRIPTION between all primers, the amount of resulting primer-dimer DESCRIPTION is reduced and the overall efficiency of the reaction is DESCRIPTION increased. Resulting primers are also screened to ensure DESCRIPTION they do not have large Tm or GC% discrepancies. DESCRIPTION DESCRIPTION Restriction Enzyme Analysis DESCRIPTION The program comes with a database of over 300 enzymes and DESCRIPTION includes an editing facility to add, delete, or modify DESCRIPTION enzymes. Enzyme analysis supports full degeneracy allowing DESCRIPTION restriction analysis of degenerate sequences. Restriction DESCRIPTION recognition sites can also include degenerate bases for DESCRIPTION enyzmes with multiple recognition sequences. The DESCRIPTION restriction results can be displayed in a table, overall DESCRIPTION restriction site map, or sequence display with marked DESCRIPTION restriction sites. DESCRIPTION DESCRIPTION Site Directed Mutagenesis DESCRIPTION The program allows for easy incorporation of point DESCRIPTION mutations and restriction sites into primers. A primer DESCRIPTION can be loaded into the mutation facility and the amino DESCRIPTION acid translation viewed. As the primer is mutated, the DESCRIPTION new translation is shown as well as the translation of the DESCRIPTION original sequence. The primer is also analyzed for DESCRIPTION restriction sites as it is mutated, showing the addition DESCRIPTION and removal of restriction sites. DESCRIPTION DESCRIPTION Sequencing Primers DESCRIPTION Sequencing primer search facilities locate sequencing DESCRIPTION primers in both the sense and anti-sense strand with high DESCRIPTION Tm’s while ensuring they contain no secondary structures DESCRIPTION or false priming sites. The multiplex tool can then be DESCRIPTION used to ensure cross-primer compatibility for use with DESCRIPTION multiplex sequencing. DESCRIPTION DESCRIPTION Primer Management Tools DESCRIPTION The program comes equipped with a Primer Database for DESCRIPTION keeping track of the primers in the lab. It supports DESCRIPTION multiple files allowing a separate file for DESCRIPTION each sequence. It allows individual primers to be named DESCRIPTION for ready identification. This is useful in keeping track DESCRIPTION of the growing list of a labs primers. The program will DESCRIPTION also print an oligo synthesis order form for any primers DESCRIPTION loaded into the database. This is convenient for ordering DESCRIPTION new primers, and re-ordering primers that are normally kept DESCRIPTION stocked. DESCRIPTION DESCRIPTION Documentation DESCRIPTION Primer Premier comes with extensive documentation. DESCRIPTION It comes with a tutorial with basic and advanced lessons DESCRIPTION covering all the aspects of PCR and sequencing primer DESCRIPTION design. The tutorial leads new users through all parts DESCRIPTION of the program. There is a professionally written DESCRIPTION reference manual with detailed information on every window DESCRIPTION as well as formulas and references for all algorithmns. DESCRIPTION The reference manual is also available on-line in the DESCRIPTION Windows version. Finally, there is a free tech support line. AUTHOR - RT - ADDRESS PREMIER Biosoft International ADDRESS 3786 Corina Way ADDRESS Palo Alto, CA 94303-4504, USA ADDRESS Tel: +1 415.856.2703 Fax: +1 415.843.1250 CONTACT sales@PremierBiosoft.com SITE WWW Server at URL http://www.PremierBiosoft.com/ OS Power Mac, Windows 3.1, NT, and 95 LANGUAGE - VOLUME - REQUIRES - COMMENTS A free demo is available for downloading COMMENTS at www.PremierBiosoft.com AC BC00522 NAME Primers! for the WWW DOMAIN Sequence analysis DOMAIN Genetic tools DOMAIN Oligomer design and synthesis DOMAIN WWW server SERVER http://www.williamstone.com/primers DESCRIPTION Free oligonucleotide design and analysis online. AUTHOR Richard Resnick, Williamstone Enterprises Inc. RA Resnick, R.; RT "Primers! for the WWW"; RL http://www.williamstone.com (1997). ADDRESS 46A Cedar St. ADDRESS Waltham, MA 02154 CONTACT rjr@williamstone.com SITE WWW Server at URL http://www.williamstone.com/primers OS All LANGUAGE Perl VOLUME n/a REQUIRES Any Graphical WWW Browser