Bioinformatics

EDITORIAL:

Masaru Tomita

Towards Computer Aided Design (CAD) of Useful Microorganisms
Bioinformatics 2001 17: 1091-1092; doi:10.1093/bioinformatics/17.12.1091 [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Hui-Hsien Chou and Michael H. Holmes

DNA sequence quality trimming and vector removal
Bioinformatics 2001 17: 1093-1104; doi:10.1093/bioinformatics/17.12.1093 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

William C. Ray, Robert S. Munson, Jr, and Charles J. Daniels

Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features
Bioinformatics 2001 17: 1105-1112; doi:10.1093/bioinformatics/17.12.1105 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouzé, and Yves Moreau

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
Bioinformatics 2001 17: 1113-1122; doi:10.1093/bioinformatics/17.12.1113 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Baris E. Suzek, Maria D. Ermolaeva, Mark Schreiber, and Steven L. Salzberg

A probabilistic method for identifying start codons in bacterial genomes
Bioinformatics 2001 17: 1123-1130; doi:10.1093/bioinformatics/17.12.1123 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Leping Li, Clarice R. Weinberg, Thomas A. Darden, and Lee G. Pedersen

Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
Bioinformatics 2001 17: 1131-1142; doi:10.1093/bioinformatics/17.12.1131 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Katsuhisa Horimoto and Hiroyuki Toh

Statistical estimation of cluster boundaries in gene expression profile data
Bioinformatics 2001 17: 1143-1151; doi:10.1093/bioinformatics/17.12.1143 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

S. Bortoluzzi, F. d’Alessi, C. Romualdi, and G. A. Danieli

Differential expression of genes coding for ribosomal proteins in different human tissues
Bioinformatics 2001 17: 1152-1157; doi:10.1093/bioinformatics/17.12.1152 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Caleb Webber and Geoffrey J. Barton

Estimation of P-values for global alignments of protein sequences
Bioinformatics 2001 17: 1158-1167; doi:10.1093/bioinformatics/17.12.1158 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Georg Fuellen, Johann-Wolfgang Wägele, and Robert Giegerich

Minimum conflict: a divide-and-conquer approach to phylogeny estimation
Bioinformatics 2001 17: 1168-1178; doi:10.1093/bioinformatics/17.12.1168 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Michael Wildpaner, Georg Schneider, Alexander Schleiffer, and Frank Eisenhaber

Taxonomy workbench
Bioinformatics 2001 17: 1179-1182; doi:10.1093/bioinformatics/17.12.1179 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andreas Wagner

How to reconstruct a large genetic network from n gene perturbations in fewer than n² easy steps
Bioinformatics 2001 17: 1183-1197; doi:10.1093/bioinformatics/17.12.1183 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Frank Kose, Wolfram Weckwerth, Thomas Linke, and Oliver Fiehn

Visualizing plant metabolomic correlation networks using clique–metabolite matrices
Bioinformatics 2001 17: 1198-1208; doi:10.1093/bioinformatics/17.12.1198 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Mark Hoebeke, Hélène Chiapello, Philippe Noirot, and Philippe Bessières

SPiD: a subtilis protein interaction database
Bioinformatics 2001 17: 1209-1212; doi:10.1093/bioinformatics/17.12.1209 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Michael V. Boland and Robert F. Murphy

A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells
Bioinformatics 2001 17: 1213-1223; doi:10.1093/bioinformatics/17.12.1213 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

DISCOVERY NOTES:

Hiromi Nishida

Evolution of amino acid biosynthesis and enzymes with broad substrate specificity
Bioinformatics 2001 17: 1224-1225; doi:10.1093/bioinformatics/17.12.1224 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Nicolas Le Novère

MELTING, computing the melting temperature of nucleic acid duplex
Bioinformatics 2001 17: 1226-1227; doi:10.1093/bioinformatics/17.12.1226 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Michael Baudis and Michael L. Cleary

Progenetix.net: an online repository for molecular cytogenetic aberration data
Bioinformatics 2001 17: 1228-1229; doi:10.1093/bioinformatics/17.12.1228 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

K. A. Jolley, E. J. Feil, M.-S. Chan, and M. C. J. Maiden

Sequence type analysis and recombinational tests (START)
Bioinformatics 2001 17: 1230-1231; doi:10.1093/bioinformatics/17.12.1230 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Theresa Zhang and Michael Zhang

Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes
Bioinformatics 2001 17: 1232-1233; doi:10.1093/bioinformatics/17.12.1232 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Thomas Junier, Marco Pagni, and Philipp Bucher

mmsearch: a motif arrangement language and search program
Bioinformatics 2001 17: 1234-1235; doi:10.1093/bioinformatics/17.12.1234 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Harpreet Singh and G. P. S. Raghava

ProPred: prediction of HLA-DR binding sites
Bioinformatics 2001 17: 1236-1237; doi:10.1093/bioinformatics/17.12.1236 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. C. Togawa, J. F. Antoniw, and J. G. L. Mullins

TMCompare: transmembrane region sequence and structure
Bioinformatics 2001 17: 1238-1239; doi:10.1093/bioinformatics/17.12.1238 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Leszek Rychlewski

ToolShop: prerelease inspections for protein structure prediction servers
Bioinformatics 2001 17: 1240-1241; doi:10.1093/bioinformatics/17.12.1240 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali, and Burkhard Rost

EVA: continuous automatic evaluation of protein structure prediction servers
Bioinformatics 2001 17: 1242-1243; doi:10.1093/bioinformatics/17.12.1242 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, and Masatoshi Nei

MEGA2: molecular evolutionary genetics analysis software
Bioinformatics 2001 17: 1244-1245; doi:10.1093/bioinformatics/17.12.1244 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hidetoshi Shimodaira and Masami Hasegawa

CONSEL: for assessing the confidence of phylogenetic tree selection
Bioinformatics 2001 17: 1246-1247; doi:10.1093/bioinformatics/17.12.1246 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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