Sequence alignment software

Doug.Eernisse at UB.CC.UMICH.EDU Doug.Eernisse at UB.CC.UMICH.EDU
Wed Sep 25 14:05:58 EST 1991


I tried posting this yesterday but haven't seen it come back as
expected, so will try again. Sorry if it is a repost.
 
 > I am looking for inexpensive or free DNA/Protein sequence alignment programs
 > for the Macintosh and would appreciate any suggestions.
 > From: Stuy at milton.u.washington.edu
 
 This is all of 4 days old now but I think it is robust and quite useful,
 if you are interested in manual alignment options:
 "Aligner" is a new freeware HyperCard 2.x stack by D. J. Eernisse, author of
 "DNA Translator" stack, for manually aligning up to 100 sequences. It was
 inspired by a stack called "MultiDNA" by Ralph Gonzalez, which allowed 
 manual alignment of six short sequences, but Aligner was
 created completely from scratch. Enhancements compared to MultiDNA include:
 1) Enlarged for use on a 640 x 480 pixel or larger monitor (automatically
 adjusts for standard small Mac screens); 2) optional help facility displays
 the function of fields or buttons as the cursor enters them; 3) accomodates
 sequences up to 30,000 bp long; 4) imports/exports multiple sequences that
 are simple return-delineated strings or in 'DNA Translator' stack string
 format (i.e., 'Name<space>AGCTGAI<rtn>'); 5) interleave formatting and
 number lines automatically adjust for the number of sequences imported; 6) a
 different stack design substantially decreases the time required to switch
 between sequences to be edited; 7) can toggle between match characters
 (dashes) to the first sequence and no match characters; 8) optionally speaks
 nucleotide characters during keyboard entry or after entry starting from the
 current insertion point; 9) converts case (lower <-> UPPER) globally; 10)
 custom menus.
 
 This stack is distributed separately or as part of the more extensive
 DNA Translator stack package. The best way to get the most current version
 of either stack is via anonymous ftp to "ub.cc.umich.edu" then "cd gdef" and
 "get aligner" or "get dnastack" for this stack only or the entire package,
 respectively. Aligner by itself is about 85 K uncompressed, including sample
 data. This stack is only free for noncommercial use and is not public
 domain. It is copyrighted 1991 by D. J. Eernisse, and uses some XFCN
 resources copyrighted by Nigel Perry with similar copyright restrictions
 (see DNA Translator stack script for details).
 
 Let me know if you find it useful.
 
 Doug Eernisse
 Email: usergdef at ub.cc.umich.edu (internet) or usergdef at umichub (bitnet)
 Mailing address: Museum of Zoology, Univ. of Michigan, Ann Arbor, MI 48109




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