Fasta 2.0.53 and 3.0.4 Scan a protein or DNA sequence library for similar sequences Copyright 1988, 1991, 1992, 1993, 1994 1995, by William R. Pearson and the University of Virginia. All rights reserved. The FASTA program and documentation may not be sold or incorporated into a commercial product, in whole or in part, without written consent of William R. Pearson and the University of Virginia. For further information regarding permission for use or reproduction, please contact: David Hudson Assistant Provost for Research University of Virginia P.O. Box 9025 Charlottesville, VA 22906-9025 (804) 924-6853 The Fasta programs are used to scan a protein or DNA sequence library for similar sequences. Currently we provide two versions. Fasta 2.0.x is the standard version. Fasta 3.0.x is an enhanced and partially parallelized version. The parallel programs Fasta3_t, Fastx3_t, Ssearch3_t and Tfasta3_t are also availabled. How to prepare your account for using the Fasta programs: The Fasta programs require the environment variable $FASTLIBS to be set. You can either set it in each session or set it permanently in your .cshrc.user file. To set it in each session type: > setenv FASTLIBS /usr/local/Fasta/fastgbs To set it permanently put the following line in your .cshrc.user file: > setenv FASTLIBS /usr/local/Fasta/fastgbs All Fasta executables are in the directory /usr/local/Fasta/bin We have already put this path in the general path on the Challenge. Important: To prevent a mixing up of Fasta and GCG program versions we capitalized the first letters of some of the Fasta programs. The following programs are coming with the Fasta program package: Fasta Version 2.0.53: Fasta* align* garnier* plalign* randseq* Lfasta* align0* grease* plfasta* relate* Tfasta* bestscor* lalign* prdf* ssearch* Ffastx* fromgb* pclfasta* prss* tgrease* Fasta Version 3.0.4: Fasta3* Fastx3* Ssearch3* Tfasta3* Multithreaded (Parallel) versions are now available: fasta3_t* fastx3_t* ssearch3_t* tfasta3_t* tfastx3_t* Fasta sequence format: Important: DO NOT USE GCG FORMATTED SEQUENCES! You can convert GCG formatted sequences to Fasta format with the GCG program tofasta (of course you have to start GCG first to use tofasta). The format of the sequences should be according to Fasta standards. Here are some examples: bovgh.seq bovprl.rev bovprl.seq egmsmg.aa lcbo.aa mchu.aa mgstm1.aa mgstm1.eeq mgstm1.rev mgstm1.seq musplfm.aa musplfm.vms mwkw.aa mwrtc1.aa oohu.aa qrhuld.aa Fasta programs know or think they know - read the manual for details - wether you have a nucleotide or amino acid sequence. Accordingly, in Fasta you will only be able to choose among the respective databases - see below for details - A+B for nucleotides or C-G for amino acids. In case of Tfasta it's the other way around. Fasta databases: Currently Fasta can search the non redundant DNA (Embl and GenBank), the non redundant Protein (Swissprot, Pir+Nrl3D, Trembl) databases and the database updates at the ZI. The respective abbreviations are: A for nr DNA B for DNA updates C for nr Protein D for Protein updates E for Swissprot F for Pir and Nrl3D G for Trembl Press > here < for more information on the non redundant databases. Fasta documentation Documents Version 2.0.x: Readme.v20 Readme.v20u5 Fasta20.txt Format.txt Documents Version 3.0.x: Readme.v30 Man pages 2.0.x: Fasta align lalign prss prdf ssearch randseq Man pages 3.0.x: Fasta3