Syngene v1.1 ------------ Syngene is a tool for designing oligonucleotides for gene synthesis. Given a protein sequence and a set of codon bias data, Syngene outputs lists of oligos of specified length which will assemble to form an appropriate coding sequence. What is Gene Synthesis? ----------------------- Gene synthesis is a technique for assembling a large double-stranded DNA of interest from individual oligonucleotides. In brief, the oligonucleotides are pooled and assembled in a reaction analogous to PCR. The oligos for one strand of the DNA are staggered relative to those for the other strand, so that overlapping oligos will hybridise to one another in the pool. The resulting assemblies serve as templates for DNA polymerases. Several cycles of oligo assembly and elongation result in a full length DNA. The method is useful for making genes or other DNAs for a variety of purposes - for example, producing genes encoding a protein from one organism with the codon bias of another organism, for heterologous expression. What does Syngene do? --------------------- Syngene takes a protein sequence file and a codon bias file and produces a series of oligo sequences which will assemble to form a gene encoding the protein using the specified bias. The protein sequence is accepted in the form of a text file; the program will use all letters, upper or lower case, from this file, discarding all other characters. The codon bias file is also a text file which, for each amino acid, gives the frequencies with which given codons occur for that amino acid. For each amino acid in the protein sequence, Syngene selects from the possible codons according to their probabilities. Syngene can also exclude certain restriction enzyme sites from occurring in the finished DNA so that these sites may be used for cloning. To this end, it uses a further file of restriction enzyme site definitions called RELibrary, new definitions may be strightforwardly added to this file if necessary. v1.0 of Syngene can only find palindromic restriction sites. What does Syngene output? ------------------------- Syngene usually outputs two lists of oligos to two text files (one for forward oligos and one for reverse) and to stdout. Warnings are given for letters in the protein sequence which are not found in the codon bias definition file, but these do not halt output. Contents of the tar Archive --------------------------- drwxr-sr-x 2788/40 0 May 28 09:35 1999 Syngene/ -rw-r--r-- 2788/40 2401 Feb 3 09:34 1999 Syngene/RELibrary -rw-r--r-- 2788/40 364 Feb 3 09:34 1999 Syngene/dicty.bias -rwxr-xr-x 2788/40 36268 May 27 17:58 1999 Syngene/syngene -rw-r--r-- 2788/40 3049 May 28 09:34 1999 Syngene/syngene.txt -rwxr--r-- 2788/40 2845 May 27 19:08 1999 Syngene/cconverter -rw-r--r-- 2788/40 13224 May 27 17:54 1999 Syngene/syngene.c -rw-r--r-- 2788/40 573 May 27 17:53 1999 Syngene/arath.bias -rw-r--r-- 2788/40 538 May 27 17:53 1999 Syngene/celegans.bias -rw-r--r-- 2788/40 594 May 27 17:53 1999 Syngene/drome.bias -rw-r--r-- 2788/40 580 May 27 17:53 1999 Syngene/ecoli.bias -rw-r--r-- 2788/40 587 May 27 17:53 1999 Syngene/hsapiens.bias -rw-r--r-- 2788/40 566 May 27 17:53 1999 Syngene/ntabac.bias -rw-r--r-- 2788/40 545 May 27 17:53 1999 Syngene/scere.bias -rw-r--r-- 2788/40 566 May 27 17:53 1999 Syngene/spombe.bias To extract the contents of the tar.gz compressed archive, first run gzip (e.g.: example% gzip -d syngene.tar.gz) and then tar (e.g.: example% tar xvf syngene.tar) and the files listed above should be generated. 'syngene' is the compiled program, and 'syngene.c' is the C source code. 'RELibrary' contains data about restriction enzyme sites. '.bias' files contain codon bias data for a range of organisms. 'cconverter' is a Perl program to convert GCG codon bias files into the format accepted by syngene. Miscellaneous ------------- Syngene was originally written by Guy Cavet and compiled under UNIX (SunOS 5.6) using gcc. Please acknowledge Guy Cavet, Biochemistry Dept. Stanford University. It may be freely distributed in source or compiled forms as long as all contributors are acknowledged and that this document accompanies it. No warranty is implied and the author or authors may not be held liable for any consequences of the use or distribution of the software. Comments or suggestions to gcavet@cmgm.stanford.edu (29 January 1999). V1.1 27th May 1999 - added capacity to deal with comments in codon bias files, and made a few invisible tweaks.