-
Pierre Baldi, Soren Brunak, Yves Chauvin,
Anders Krogh (1996),
"Naturally occurring nucleosome positioning
signals in human exons and introns",
Journal of Molecular Biology, 263: 503-510.
[abstract]
[ PDF]
-
C Barry, G Fichant, A Kalogeropoulos, Y Quentin (1996),
"A computer filtering method to drive out tiny genes from the yeast
genome",
Yeast, 12(11):1163-1178.
[ Medline entry]
-
Craig J. Benham (1996),
"Computation of DNA structural variability
- a new predictor of DNA regulatory regions",
Computer Applications in Biosciences,
12(5): 375-381.
[ abstract]
-
P. Bucher, J.W. Fickett, A. Hatzigeorgiou (1996),
"Computational analysis of transcriptional regulatory
elements: a field in flux",
Computer Applications in Biosciences,
12(5): 361-362.
-
M. Burset, R. Guigo (1996),
"Evaluation of gene structure prediction programs",
Genomics, 34(3): 353-367 (June 15)
[ Medline entry ]
[ PDF]
[the data can be found at
http://www.imim.es/GeneIdentification/Evaluation/Index.html ; the
following programs are evaluated:GeneID, GeneID+, SORFIND, GParser2,
GParser3, GRAIL II, GAP, GenLang, FgeneH, XPound.]
-
J. -M. Claverie, S. Audic (1996)
"The statistical significance
of nucleotide position-weight matrix matches",
Computer Applications in Biosciences, 12: 431-439.
[abstract]
-
SJ de Souza, M Long, L Schoenbach, SW Roy, W Gilbert (1996),
"Intron positions correlate with module boundaries in ancient
proteins",
Proceedings of the National Academy of Sciences, 93:14632-14636.
[ Medline entry]
-
J.W. Fickett (1996),
"Quantitative discrimination of MEF2 sites",
Molecular and Cellular Biology, 16(1): 437-441.
[abstract]
-
J.W. Fickett (1996),
"Coordinate positioning of MEF2 and myogenin binding sites",
Gene, 172(1): GC19-32.
-
J.W. Fickett (1996),
"The gene identification problem: an overview for developers",
Computer & Chemistry, 20: 103-118
[ abstract]
[ PDF ]
-
J.W. Fickett (1996),
"Finding genes by computer: the state of the art",
Trends in Genetics, 12(8): 316-320.
[ abstract]
-
Mikhail S. Gelfand, Andrey A. Mironov,
Pavel A. Pevzner (1996):
"Gene recognition via spliced sequence alignment",
Proceedings of the National Academy of Sciences (USA), 93(17): 9061-9066.
[ abstract]
[ Medline entry]
[home page of PROCRUSTE program at
http://www-hto.usc.edu/software/procrustes/ ]
-
M.S. Gelfand, L.I. Podolsky, T.V. Astakhova, and M.A. Roytberg (1996),
"Recognition of Genes in Human DNA Sequences",
Journal of Computational Biology: 3(2):223-234.
[ abstract]
[ Medline entry]
-
Robert Giegerich, Folker Meyer, and Chris Schleiermacher (1996)
"GeneFisher - Software support for the detection of postulated genes"
in ISMB96, 68-77.
-
S.M. Hebsgaard, P.G. Korning, N. Tolskup, J. Engelbrecht,
P. Rouzé, S. Brunak (1996),
"Splice
site prediction in Arabidopsis theliana pre-mRNA by
combining local and global sequence information",
Nucleic Acids Research, 24(17): 3439-3452.
[abstract]
[ PDF ]
[NetPlantGene homapage at
http://www.cbs.dtu.dk/NetPlantGene.html from
Center for Biological Sequence Analysis,
The Technical University of Denmark.]
-
G.B. Hutchinson (1996),
"The prediction of vertebrate promoter
regions using differential hexamer frequency analysis",
Computer Applications in Biosciences,
12(5): 391-398.
[abstract]
[ PROMFIND is at:
http://www.rabbithutch.com/ ]
-
H. Karas, R. Knuppel, W. Schulz, H. Sklenar, E. Wingender (1996),
"Combining
structural analysis of DNA with search routines for the
detection of transcription regulatory elements",
Computer Applications in Biosciences,
12(5): 441-446 (1996).
[
abstract]
-
David Kulp,
David Haussler,
Martin G. Reese,
and Frank H. Eeckman (1996),
"A generalized hidden Markov model for
the recognition of human genes in DNA",
in ISMB96, 134-142.
[abstract]
[ Medline entry]
[ GENIE is at:
http://www.fruitfly.org/seq_tools/genie.html ]
-
J.D. McIninch, W.S. Hayes, M.Borodovsky (1996),
"Applications of GeneMark in Multispecies Environments",
in ISMB96, 166-175.
[ Medline entry ]
-
S. Matis, Y. Xu, M. Shah, X. Guan, J.R. Einstein,
R. Mural, E. Uberbacher (1996)
"Detection of RNA polymerase II promoters and polyadenylation sites
in human DNA",
Computer & Chemistry, 20: 135-140.
-
L. Milanesi, M. Muselli, P. Arrigo (1996),
"Hamming Clustering method for
signals prediction in 5' and 3' regions of eukaryotic genes",
Computer Applications in Biosciences,
12(5): 399-404.
[ abstract]
-
J.L. Oliver, A. Marin (1996),
"A relationship between GC content and
coding-sequence length",
Journal of Molecular Evolution, 43: 216-223.
[abstract]
-
Anders Gorm Pedersen,
Pierre Baldi,
Søren Brunak, and
Yves Chauvan (1996),
"Characterization of prokaryotic and eukaryotic promoters
using hidden Markov models",
in ISMB96, 182-191.
[ abstract]
[ Medline entry]
[ PDF ]
-
G Pesole, G Grillo, S Liuni (1996),
"Databases of mRNA untranslated regions for metazoa",
Computer & Chemistry, 20(1):141-144.
[ Medline entry ]
-
Graziano Pesole, Marcella Attimonelli, Cecilia Saccone (1996),
"Linguistic analysis of nucleotide sequences: algorithms for
pattern recognition and analysis of codon strategy",
Methods in Enzymology, 266: 281-294 .
-
I. Ponte, C. Monsalves, M. Cabanas,
P. Martinez, P. Suau (1996),
"Sequence simplicity and evolution of the 3' untranslated
region of the histone H1o gene",
Journal of Molecular Evolution, 43: 125-134.
[abstract]
-
DS Prestridge (1996),
"SIGNAL SCAN 4.0: additional databases and sequence formats",
Computer Applications in Biosciences, 12(2):157-160.
[ Medline entry]
-
I.B. Rogozin, L. Milanesi and NA. Kolchanov (1996),
"Gene structure prediction using information on homologous
protein sequence",
Computer Applications in Biosciences,
12(3): 161-170.
[abstract]
[see also WebGene
a web interface for several coding region recognition programs,
at
http://www.itba.mi.cnr.it/webgene ]
-
D.A. Rosenblueth, D. Thieffry, A.M. Huerta, H. Salgado,
J. Collado-Vides (1996),
"Syntactic recognition of regulatory regions in
Escherichia coli",
Computer Applications in Biosciences,
12(5): 415-422 (1996)
[abstract]
-
Steven Salzberg, Xin Chen, John Henderson, and Kenneth Fasman
(1996),
"Finding genes in DNA using decision trees and dynamic programming",
in ISMB96, 201-210.
[ abstract]
[ Medline entry]
-
PM Sharp, MC Smith (1996),
"Identifying bacterial genes--a cautionary tale",
Microbiology, 142(4):717-718.
-
M Termier, A Kalogeropoulos (1996),
"Discrimination between fortuitous and biologically constrained
open reading frames in DNA sequences of Saccharomyces cerevisiae",
Yeast, 12(4):369-384.
-
E.N. Trifonov (1996),
"Interfering
contexts of regulatory sequence elements",
Computer Applications in Biosciences,
12(5): 423-429.
[ abstract]
-
Edward C. Uberbacher, Ying Xu, Richard J. Mural (1996),
"Discovering and
understanding genes in human DNA sequence using GRAIL",
Methods in Enzymology, 266: 259-281 .
-
T.D. Wu (1996)
"A segment-based dynamic programming algorithm for predicting gene",
Journal of Computational Biology, 3: 375-394.
[abstract]
-
Ying Xu, Edward C. Uberbacher (1996),
"Gene prediction by pattern recognition and homology search",
in
ISMB96, 241-251.
[abstract]
[ Medline entry]
-
T. Yada, M. Hirosawa (1996),
"Detection of short protein coding regions within the
cyanobacterium genome: Application of the Hidden Markov Model",
DNA Research, 3:355-361.
[ Medline entry]
-
Tetsushi Yada and Makoto Hirosawa (1996),
"Gene recognition in Cyanobacterium genomic sequence data
using the midden Markov model",
in ISMB96, 252-260.
[ Medline entry]
-
T Yada, M Ishikawa, H Tanaka, K Asai (1996),
"Extraction of hidden Markov model representations of
signal patterns in DNA sequences",
Pacific Symposium on Biocomputing, 686-696.
1996