Volume 32; Issue Web Server

Nucleic Acids Research

Volume 32; Issue Web Server
1

Gene2Oligo: oligonucleotide design for in vitro gene synthesis

Rouillard, J.-M., Lee, W., Truan, G., Gao, X., Zhou, X., Gulari, E.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 100 KB
english, 2004
2

ClusPro: a fully automated algorithm for protein-protein docking

Comeau, S. R., Gatchell, D. W., Vajda, S., Camacho, C. J.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 250 KB
english, 2004
6

DIALIGN: multiple DNA and protein sequence alignment at BiBiServ

Morgenstern, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 396 KB
english, 2004
12

LINKER: a web server to generate peptide sequences with extended conformation

Xue, F., Gu, Z., Feng, J.-a.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 365 KB
english, 2004
15

PrediSi: prediction of signal peptides and their cleavage positions

Hiller, K., Grote, A., Scheer, M., Munch, R., Jahn, D.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 574 KB
english, 2004
17

CVTree: a phylogenetic tree reconstruction tool based on whole genomes

Qi, J., Luo, H., Hao, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 248 KB
english, 2004
20

CARNAC: folding families of related RNAs

Touzet, H., Perriquet, O.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 255 KB
english, 2004
21

A web-based genotyping resource for viral sequences

Rozanov, M., Plikat, U., Chappey, C., Kochergin, A., Tatusova, T.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 279 KB
english, 2004
24

AUGUSTUS: a web server for gene finding in eukaryotes

Stanke, M., Steinkamp, R., Waack, S., Morgenstern, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 91 KB
english, 2004
30

The PredictProtein server

Rost, B., Yachdav, G., Liu, J.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 82 KB
english, 2004
31

PlasMapper: a web server for drawing and auto-annotating plasmid maps

Dong, X., Stothard, P., Forsythe, I. J., Wishart, D. S.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 963 KB
english, 2004
32

CD-Search: protein domain annotations on the fly

Marchler-Bauer, A., Bryant, S. H.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 571 KB
english, 2004
34

CE-MC: a multiple protein structure alignment server

Guda, C., Lu, S., Scheeff, E. D., Bourne, P. E., Shindyalov, I. N.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 398 KB
english, 2004
37

CHOP: parsing proteins into structural domains

Liu, J., Rost, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 99 KB
english, 2004
38

COLORADO3D, a web server for the visual analysis of protein structures

Sasin, J. M., Bujnicki, J. M.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 135 KB
english, 2004
41

POBO, transcription factor binding site verification with bootstrapping

Kankainen, M., Holm, L.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 698 KB
english, 2004
43

Detecting distant homology with Meta-BASIC

Ginalski, K., von Grotthuss, M., Grishin, N. V., Rychlewski, L.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 264 KB
english, 2004
44

rVISTA 2.0: evolutionary analysis of transcription factor binding sites

Loots, G. G., Ovcharenko, I.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 274 KB
english, 2004
48

Sfold web server for statistical folding and rational design of nucleic acids

Ding, Y., Chan, C. Y., Lawrence, C. E.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 214 KB
english, 2004
52

TROD: T7 RNAi Oligo Designer

Dudek, P., Picard, D.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 180 KB
english, 2004
53

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences

Brudno, M., Steinkamp, R., Morgenstern, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 230 KB
english, 2004
54

Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins

Ahmad, S., Sarai, A.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 83 KB
english, 2004
58

The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update

Huynh, T., Rigoutsos, I.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 553 KB
english, 2004
61

GDAP: a web tool for genome-wide protein disulfide bond prediction

O'Connor, B. D., Yeates, T. O.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 357 KB
english, 2004
63

AGenDA: gene prediction by cross-species sequence comparison

Taher, L., Rinner, O., Garg, S., Sczyrba, A., Morgenstern, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 281 KB
english, 2004
65

SCit: web tools for protein side chain conformation analysis

Gautier, R., Camproux, A.-C., Tuffery, P.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 634 KB
english, 2004
66

FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web

Shapiro, J., Brutlag, D.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 709 KB
english, 2004
68

SledgeHMMER: a web server for batch searching the Pfam database

Chukkapalli, G., Guda, C., Subramaniam, S.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 148 KB
english, 2004
69

iMolTalk: an interactive, internet-based protein structure analysis server

Diemand, A. V., Scheib, H.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 529 KB
english, 2004
72

GOblet: a platform for Gene Ontology annotation of anonymous sequence data

Groth, D., Lehrach, H., Hennig, S.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 475 KB
english, 2004
73

DEQOR: a web-based tool for the design and quality control of siRNAs

Henschel, A., Buchholz, F., Habermann, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 464 KB
english, 2004
82

MotifViz: an analysis and visualization tool for motif discovery

Fu, Y., Frith, M. C., Haverty, P. M., Weng, Z.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 95 KB
english, 2004
83

NLProt: extracting protein names and sequences from papers

Mika, S., Rost, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 206 KB
english, 2004
84

PDA: a pipeline to explore and estimate polymorphism in large DNA databases

Casillas, S., Barbadilla, A.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 168 KB
english, 2004
85

FATCAT: a web server for flexible structure comparison and structure similarity searching

Ye, Y., Godzik, A.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 450 KB
english, 2004
87

PromoSer: improvements to the algorithm, visualization and accessibility

Halees, A. S., Weng, Z.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 205 KB
english, 2004
88

ProteinDBS: a real-time retrieval system for protein structure comparison

Shyu, C.-R., Chi, P.-H., Scott, G., Xu, D.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 882 KB
english, 2004
90

LOCnet and LOCtarget: sub-cellular localization for structural genomics targets

Nair, R., Rost, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 102 KB
english, 2004
91

ILM: a web server for predicting RNA secondary structures with pseudoknots

Ruan, J., Stormo, G. D., Zhang, W.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 191 KB
english, 2004
92

RDfolder: a web server for prediction of RNA secondary structure

Ying, X., Luo, H., Luo, J., Li, W.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 154 KB
english, 2004
95

A web server for performing electronic PCR

Rotmistrovsky, K., Jang, W., Schuler, G. D.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 96 KB
english, 2004
98

PubCrawler: keeping up comfortably with PubMed and GenBank

Hokamp, K., Wolfe, K. H.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 474 KB
english, 2004
100

FAN: fingerprint analysis of nucleotide sequences

Maudling, N., Attwood, T. K.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 467 KB
english, 2004
103

WebInterViewer: visualizing and analyzing molecular interaction networks

Han, K., Ju, B.-H., Jung, H.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 852 KB
english, 2004
105

Complexity: an internet resource for analysis of DNA sequence complexity

Orlov, Y. L., Potapov, V. N.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 312 KB
english, 2004
106

MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments

Ray, W. C.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 527 KB
english, 2004
108

ADVICE: Automated Detection and Validation of Interaction by Co-Evolution

Tan, S.-H., Zhang, Z., Ng, S.-K.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 229 KB
english, 2004
109

PepBuild: a web server for building structure data of peptides/proteins

Singh, B.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 442 KB
english, 2004
114

RECON: a program for prediction of nucleosome formation potential

Levitsky, V. G.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 214 KB
english, 2004
124

EDITORIAL

Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 22 KB
english, 2004
127

MITOPRED: a web server for the prediction of mitochondrial proteins

Guda, C., Guda, P., Fahy, E., Subramaniam, S.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 135 KB
english, 2004
129

CREME: Cis-Regulatory Module Explorer for the human genome

Sharan, R., Ben-Hur, A., Loots, G. G., Ovcharenko, I.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 423 KB
english, 2004
135

The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences

Helmberg, W., Dunivin, R., Feolo, M.
Journal:
Nucleic Acids Research
Year:
2004
Language:
english
File:
PDF, 384 KB
english, 2004