Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00092 NAME CAP DOMAIN Contig assembly software DESCRIPTION Contig Assembly Program AUTHOR Xiaoqiu Huang RA Huang X.; RT "A Contig Assembly Program Based on Sensitive RT Detection of Fragment Overlaps."; RL Genomics 14:18-25(1992). RX Medline; 93052293. RX SeqAnalRef; HUAX9203. ADDRESS Xiaoqiu Huang Department of Computer Science ADDRESS Michigan Technological University Houghton, MI 49931, USA CONTACT huang@cs.mtu.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/align SITE-CONTACT D Gilbert : gilbertd@cricket.bio.indiana.edu OS Sun workstations LANGUAGE C VOLUME - COMMENTS The distribution of the program is granted COMMENTS provided no charge is made and the copyright COMMENTS notice is included. Proper attribution of the COMMENTS author as the source of the software would be COMMENTS appreciated. AC BC00258 NAME STADEN DOMAIN Contig assembly software DOMAIN Sequence analysis DESCRIPTION Staden Package Automated Sequence Input, Editing DESCRIPTION and Analysis AUTHOR Staden R. RA Dear S., Staden R.; RT "A sequence assembly and editing program for efficient management RT of large projects."; RL Nucleic Acids Res. 19:3907-3911(1991). RX Medline; 91319550. RX SeqAnalRef; DEAS9101. RT "A standard file format for data from DNA sequencing RT instruments."; RL DNA Seq. 3:107-110(1992). RX Medline; 93091241. RX SeqAnalRef; DEAS9301. RA Staden R.; RT "Finding protein coding regions in genomic sequences."; RL Meth. Enzymol. 183:163-180(1990). RX Medline; 90190365. RX SeqAnalRef; STAR9001. RA Staden R.; RT "Searching for patterns in protein and nucleic acid sequences."; RL Meth. Enzymol. 183:193-211(1990). RX Medline; 90190367. RX SeqAnalRef; STAR9002. RA Staden R.; RT "Screening protein and nucleic acid sequences against libraries RT of patterns."; RL DNA Seq. 1:369-374(1991). RX Medline; 92119325. RX SeqAnalRef; STAR9101. RA Staden R., Dear S.; RT "Indexing the sequence libraries: software providing a common RT indexing system for all the standard sequence libraries."; RL DNA Seq. 3:99-105(1992). RX Medline; 93091251. RX SeqAnalRef; STAR9201. RA Dear, S. and Staden, R. RT A standard file format for data from DNA sequencing instruments. RL DNA Sequence 3, 107-110 (1992). RA Staden R.; RT "Software for sequence analysis."; RL Genome News 13:21-23(1993). RA Bonfield J.K., Smith K.F., Staden R.; RT "A New DNA Sequence Assembly Program."; RL Nucleic Acids Res. 23:4992-4999(1995). RA Bonfield, J.K. and Staden, R. RT The application of numerical estimates of base calling accuracy RT to DNA sequencing projects. RL Nucleic Acids Res. 23, 1406-1410 (1995). RA Bonfield, J.K. and Staden, R. RT Experiment files and their application during large-scale RT sequencing projects. RL DNA Sequence 6, 109-117 (1996). ADDRESS Medical Research Council, Cambridge, UK. CONTACT Rodger Staden RS@mrc-lmb.cam.ac.uk SITE WWW Server at URL http://www.mrc-lmb.cam.ac.uk/pubseq/ SITE-CONTACT Rodger Staden RS@mrc-lmb.cam.ac.uk OS Sun SPARC10 (solaris 2.5) eg SPARCstation 10/30 OS DEC ALPHA (Digital Unix 3.0/4.0) eg DEC 3000/500 OS SGI RIX) eg Indigo R4000 OS Linux 2.0 (Intel systems only) LANGUAGE FORTRAN, C, Xwindow, Tcl VOLUME -