1: Im eo, Chee W, Lim hj, Bender M, Tsai hm, Yang so, Lee H
Download 12.14 Mb.
|
|
PMID: 12824412 [PubMed - indexed for MEDLINE]
DePIE: Designing Primers for Protein Interaction Experiments. Nucleic Acids Res. 2003 Jul 1;31(13):3755-7. PMID: 12824411 [PubMed - indexed for MEDLINE] 9355: Chen SH, Lin CY, Cho CS, Lo CZ, Hsiung CA. Primer Design Assistant (PDA): A web-based primer design tool. Nucleic Acids Res. 2003 Jul 1;31(13):3751-4. PMID: 12824410 [PubMed - indexed for MEDLINE] 9356: Emrich SJ, Lowe M, Delcher AL. PROBEmer: A web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res. 2003 Jul 1;31(13):3746-50. PMID: 12824409 [PubMed - indexed for MEDLINE] 9357: Foissac S, Bardou P, Moisan A, Cros MJ, Schiex T. EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3742-5. PMID: 12824408 [PubMed - indexed for MEDLINE]
FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3738-41. PMID: 12824407 [PubMed - indexed for MEDLINE]
Bioverse: Functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res. 2003 Jul 1;31(13):3736-7. PMID: 12824406 [PubMed - indexed for MEDLINE]
DNannotator: Annotation software tool kit for regional genomic sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3729-35. PMID: 12824405 [PubMed - indexed for MEDLINE] 9361: Sugawara H, Miyazaki S. AHMII: Agent to Help Microbial Information Integration. Nucleic Acids Res. 2003 Jul 1;31(13):3727-8. PMID: 12824404 [PubMed - indexed for MEDLINE] 9362: Bocs S, Cruveiller S, Vallenet D, Nuel G, Medigue C. AMIGene: Annotation of MIcrobial Genes. Nucleic Acids Res. 2003 Jul 1;31(13):3723-6. PMID: 12824403 [PubMed - indexed for MEDLINE] 9363: Enault F, Suhre K, Poirot O, Abergel C, Claverie JM. Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. Nucleic Acids Res. 2003 Jul 1;31(13):3720-2. PMID: 12824402 [PubMed - indexed for MEDLINE]
ESTAnnotator: A tool for high throughput EST annotation. Nucleic Acids Res. 2003 Jul 1;31(13):3716-9. PMID: 12824401 [PubMed - indexed for MEDLINE] 9365: Hennig S, Groth D, Lehrach H. Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Res. 2003 Jul 1;31(13):3712-5. PMID: 12824400 [PubMed - indexed for MEDLINE] 9366: Brannetti B, Helmer-Citterich M. iSPOT: A web tool to infer the interaction specificity of families of protein modules. Nucleic Acids Res. 2003 Jul 1;31(13):3709-11. PMID: 12824399 [PubMed - indexed for MEDLINE]
GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res. 2003 Jul 1;31(13):3701-8. PMID: 12824398 [PubMed - indexed for MEDLINE] 9368: Taylor PD, Attwood TK, Flower DR. BPROMPT: A consensus server for membrane protein prediction. Nucleic Acids Res. 2003 Jul 1;31(13):3698-700. PMID: 12824397 [PubMed - indexed for MEDLINE] 9369: Cai CZ, Han LY, Ji ZL, Chen X, Chen YZ. SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res. 2003 Jul 1;31(13):3692-7. PMID: 12824396 [PubMed - indexed for MEDLINE]
NEBcutter: A program to cleave DNA with restriction enzymes. Nucleic Acids Res. 2003 Jul 1;31(13):3688-91. PMID: 12824395 [PubMed - indexed for MEDLINE] 9371: Vlahovicek K, Kajan L, Pongor S. DNA analysis servers: plot.it, bend.it, model.it and IS. Nucleic Acids Res. 2003 Jul 1;31(13):3686-7. PMID: 12824394 [PubMed - indexed for MEDLINE] 9372: Gal M, Katz T, Ovadia A, Yagil G. TRACTS: A program to map oligopurine.oligopyrimidine and other binary DNA tracts. Nucleic Acids Res. 2003 Jul 1;31(13):3682-5. PMID: 12824393 [PubMed - indexed for MEDLINE] 9373: Richard H, Nuel G. SPA: Simple web tool to assess statistical significance of DNA patterns. Nucleic Acids Res. 2003 Jul 1;31(13):3679-81. PMID: 12824392 [PubMed - indexed for MEDLINE] 9374: Kolpakov R, Bana G, Kucherov G. mreps: Efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res. 2003 Jul 1;31(13):3672-8. PMID: 12824391 [PubMed - indexed for MEDLINE] 9375: Robelin D, Richard H, Prum B. SIC: A tool to detect short inverted segments in a biological sequence. Nucleic Acids Res. 2003 Jul 1;31(13):3669-71. PMID: 12824390 [PubMed - indexed for MEDLINE] 9376: Frith MC, Li MC, Weng Z. Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3666-8. PMID: 12824389 [PubMed - indexed for MEDLINE] 9377: Yang G, Hall TC. MAK, a computational tool kit for automated MITE analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3659-65. PMID: 12824388 [PubMed - indexed for MEDLINE] 9378: Yadav G, Gokhale RS, Mohanty D. SEARCHPKS: A program for detection and analysis of polyketide synthase domains. Nucleic Acids Res. 2003 Jul 1;31(13):3654-8. PMID: 12824387 [PubMed - indexed for MEDLINE] 9379: Farre D, Roset R, Huerta M, Adsuara JE, Rosello L, Alba MM, Messeguer X. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic Acids Res. 2003 Jul 1;31(13):3651-3. PMID: 12824386 [PubMed - indexed for MEDLINE]
The web server of IBM's Bioinformatics and Pattern Discovery group. Nucleic Acids Res. 2003 Jul 1;31(13):3645-50. PMID: 12824385 [PubMed - indexed for MEDLINE] 9381: Kernytsky A, Rost B. Static benchmarking of membrane helix predictions. Nucleic Acids Res. 2003 Jul 1;31(13):3642-4. PMID: 12824384 [PubMed - indexed for MEDLINE] 9382: Obenauer JC, Cantley LC, Yaffe MB. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 2003 Jul 1;31(13):3635-41. PMID: 12824383 [PubMed - indexed for MEDLINE]
Schneider G, Wildpaner M. Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Nucleic Acids Res. 2003 Jul 1;31(13):3631-4. PMID: 12824382 [PubMed - indexed for MEDLINE] 9384: Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferre F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Kuster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 2003 Jul 1;31(13):3625-30. PMID: 12824381 [PubMed - indexed for MEDLINE]
MHCPred: A server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res. 2003 Jul 1;31(13):3621-4. PMID: 12824380 [PubMed - indexed for MEDLINE] 9386: Ambrosini G, Praz V, Jagannathan V, Bucher P. Signal search analysis server. Nucleic Acids Res. 2003 Jul 1;31(13):3618-20. PMID: 12824379 [PubMed - indexed for MEDLINE] 9387: Gardy JL, Spencer C, Wang K, Ester M, Tusnady GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS. PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res. 2003 Jul 1;31(13):3613-7. PMID: 12824378 [PubMed - indexed for MEDLINE] 9388: Grillo G, Licciulli F, Liuni S, Sbisa E, Pesole G. PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3608-12. PMID: 12824377 [PubMed - indexed for MEDLINE]
ET.
Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes. Nucleic Acids Res. 2003 Jul 1;31(13):3605-7. PMID: 12824376 [PubMed - indexed for MEDLINE] 9390: Majoros WH, Pertea M, Antonescu C, Salzberg SL. GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res. 2003 Jul 1;31(13):3601-4. PMID: 12824375 [PubMed - indexed for MEDLINE] 9391: Schlueter SD, Dong Q, Brendel V. GeneSeqer@PlantGDB: Gene structure prediction in plant genomes. Nucleic Acids Res. 2003 Jul 1;31(13):3597-600. PMID: 12824374 [PubMed - indexed for MEDLINE] 9392: van Helden J. Regulatory sequence analysis tools. Nucleic Acids Res. 2003 Jul 1;31(13):3593-6. PMID: 12824373 [PubMed - indexed for MEDLINE] 9393: Sosinsky A, Bonin CP, Mann RS, Honig B. Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res. 2003 Jul 1;31(13):3589-92. PMID: 12824372 [PubMed - indexed for MEDLINE]
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 2003 Jul 1;31(13):3586-8. PMID: 12824371 [PubMed - indexed for MEDLINE]
Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res. 2003 Jul 1;31(13):3580-5. PMID: 12824370 [PubMed - indexed for MEDLINE] 9396: Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E.
MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3576-9. PMID: 12824369 [PubMed - indexed for MEDLINE] 9397: Boardman PE, Oliver SG, Hubbard SJ. SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3572-5. PMID: 12824368 [PubMed - indexed for MEDLINE]
ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res. 2003 Jul 1;31(13):3568-71. PMID: 12824367 [PubMed - indexed for MEDLINE] 9399: Nekrutenko A, Chung WY, Li WH. ETOPE: Evolutionary test of predicted exons. Nucleic Acids Res. 2003 Jul 1;31(13):3564-7. PMID: 12824366 [PubMed - indexed for MEDLINE] 9400: Bajic VB, Seah SH. Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes. Nucleic Acids Res. 2003 Jul 1;31(13):3560-3. PMID: 12824365 [PubMed - indexed for MEDLINE] 9401: Halees AS, Leyfer D, Weng Z. PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res. 2003 Jul 1;31(13):3554-9. PMID: 12824364 [PubMed - indexed for MEDLINE]
FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. Nucleic Acids Res. 2003 Jul 1;31(13):3546-53. PMID: 12824363 [PubMed - indexed for MEDLINE]
PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3540-5. PMID: 12824362 [PubMed - indexed for MEDLINE] 9404: Wernersson R, Pedersen AG. RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3537-9. PMID: 12824361 [PubMed - indexed for MEDLINE] 9405: Lee BT, Tan TW, Ranganathan S. MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3533-6. PMID: 12824360 [PubMed - indexed for MEDLINE] 9406: Florea L, McClelland M, Riemer C, Schwartz S, Miller W. EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae. Nucleic Acids Res. 2003 Jul 1;31(13):3527-32. PMID: 12824359 [PubMed - indexed for MEDLINE] 9407: Bray N, Pachter L. MAVID multiple alignment server. Nucleic Acids Res. 2003 Jul 1;31(13):3525-6. PMID: 12824358 [PubMed - indexed for MEDLINE] 9408: Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A; NISC Comparative Sequencing Program; Green ED, Hardison RC, Miller W. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3518-24. PMID: 12824357 [PubMed - indexed for MEDLINE] 9409: Edwards YJ, Carver TJ, Vavouri T, Frith M, Bishop MJ, Elgar G. Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence. Nucleic Acids Res. 2003 Jul 1;31(13):3510-7. PMID: 12824356 [PubMed - indexed for MEDLINE]
SLAM web server for comparative gene finding and alignment. Nucleic Acids Res. 2003 Jul 1;31(13):3507-9. PMID: 12824355 [PubMed - indexed for MEDLINE] 9411: Poirot O, O'Toole E, Notredame C. Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. PMID: 12824354 [PubMed - indexed for MEDLINE]
CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics. Nucleic Acids Res. 2003 Jul 1;31(13):3501-2. PMID: 12824353 [PubMed - indexed for MEDLINE]
JD.
Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003 Jul 1;31(13):3497-500. PMID: 12824352 [PubMed - indexed for MEDLINE]
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res. 2003 Jul 1;31(13):3491-6. PMID: 12824351 [PubMed - indexed for MEDLINE]
REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data. Nucleic Acids Res. 2003 Jul 1;31(13):3487-90. PMID: 12824350 [PubMed - indexed for MEDLINE]
ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3483-6. PMID: 12824349 [PubMed - indexed for MEDLINE]
Gerstein M. ExpressYourself: A modular platform for processing and visualizing microarray data.
Nucleic Acids Res. 2003 Jul 1;31(13):3477-82. PMID: 12824348 [PubMed - indexed for MEDLINE] 9418: Knudsen S, Workman C, Sicheritz-Ponten T, Friis C. GenePublisher: Automated analysis of DNA microarray data. Nucleic Acids Res. 2003 Jul 1;31(13):3471-6. PMID: 12824347 [PubMed - indexed for MEDLINE] 9419: Coessens B, Thijs G, Aerts S, Marchal K, De Smet F, Engelen K, Glenisson P, Moreau Y, Mathys J, De Moor B. INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3468-70. PMID: 12824346 [PubMed - indexed for MEDLINE] 9420: Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3461-7. PMID: 12824345 [PubMed - indexed for MEDLINE]
Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 2003 Jul 1;31(13):3450-60. PMID: 12824344 [PubMed - indexed for MEDLINE] 9422: Hu YJ. GPRM: A genetic programming approach to finding common RNA secondary structure elements. Nucleic Acids Res. 2003 Jul 1;31(13):3446-9. PMID: 12824343 [PubMed - indexed for MEDLINE]
A software tool-box for analysis of regulatory RNA elements. Nucleic Acids Res. 2003 Jul 1;31(13):3441-5. PMID: 12824342 [PubMed - indexed for MEDLINE] 9424: Han K, Byun Y. PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type. Nucleic Acids Res. 2003 Jul 1;31(13):3432-40. PMID: 12824341 [PubMed - indexed for MEDLINE] 9425: Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003 Jul 1;31(13):3429-31. PMID: 12824340 [PubMed - indexed for MEDLINE] 9426: Knudsen B, Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 2003 Jul 1;31(13):3423-8. PMID: 12824339 [PubMed - indexed for MEDLINE]
RNAsoft: A suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res. 2003 Jul 1;31(13):3416-22. PMID: 12824338 [PubMed - indexed for MEDLINE] 9428: Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003 Jul 1;31(13):3406-15. PMID: 12824337 [PubMed - indexed for MEDLINE] 9429: Shanthi V, Selvarani P, Kumar ChK, Mohire CS, Sekar K. SSEP: Secondary structural elements of proteins. Nucleic Acids Res. 2003 Jul 1;31(13):3404-5. PMID: 12824336 [PubMed - indexed for MEDLINE] 9430: Bettler E, Krause R, Horn F, Vriend G. NRSAS: Nuclear Receptor Structure Analysis Servers. Nucleic Acids Res. 2003 Jul 1;31(13):3400-3. PMID: 12824335 [PubMed - indexed for MEDLINE] 9431: Perriere G, Combet C, Penel S, Blanchet C, Thioulouse J, Geourjon C, Grassot J, Charavay C, Gouy M, Duret L, Deleage G. Integrated databanks access and sequence/structure analysis services at the PBIL.
Nucleic Acids Res. 2003 Jul 1;31(13):3393-9. PMID: 12824334 [PubMed - indexed for MEDLINE] 9432: Neshich G, Togawa RC, Mancini AL, Kuser PR, Yamagishi ME, Pappas G Jr, Torres WV, Fonseca e Campos T, Ferreira LL, Luna FM, Oliveira AG, Miura RT, Inoue MK, Horita LG, de Souza DF, Dominiquini F, Alvaro A, Lima CS, Ogawa FO, Gomes GB, Palandrani JF, dos Santos GF, de Freitas EM, Mattiuz AR, Costa IC, de Almeida CL, Souza S, Baudet C, Higa RH. STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence. Nucleic Acids Res. 2003 Jul 1;31(13):3386-92. PMID: 12824333 [PubMed - indexed for MEDLINE]
SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 2003 Jul 1;31(13):3381-5. PMID: 12824332 [PubMed - indexed for MEDLINE] 9434: Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3375-80. PMID: 12824331 [PubMed - indexed for MEDLINE]
LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res. 2003 Jul 1;31(13):3370-4. PMID: 12824330 [PubMed - indexed for MEDLINE] 9436: Kawabata T. MATRAS: A program for protein 3D structure comparison. Nucleic Acids Res. 2003 Jul 1;31(13):3367-9. PMID: 12824329 [PubMed - indexed for MEDLINE] 9437: Cavallo L, Kleinjung J, Fraternali F. POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res. 2003 Jul 1;31(13):3364-6. PMID: 12824328 [PubMed - indexed for MEDLINE]
Servers for sequence-structure relationship analysis and prediction. Nucleic Acids Res. 2003 Jul 1;31(13):3359-63. PMID: 12824327 [PubMed - indexed for MEDLINE] 9439: Hussain AS, Kumar ChK, Rajesh CK, Sheik SS, Sekar K. SEM (Symmetry Equivalent Molecules): A web-based GUI to generate and visualize the macromolecules. Nucleic Acids Res. 2003 Jul 1;31(13):3356-8. PMID: 12824326 [PubMed - indexed for MEDLINE]
CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Res. 2003 Jul 1;31(13):3352-5. PMID: 12824325 [PubMed - indexed for MEDLINE] 9441: Gabdoulline RR, Wade RC, Walther D. MolSurfer: A macromolecular interface navigator. Nucleic Acids Res. 2003 Jul 1;31(13):3349-51. PMID: 12824324 [PubMed - indexed for MEDLINE] 9442: Babu MM. NCI: A server to identify non-canonical interactions in protein structures. Nucleic Acids Res. 2003 Jul 1;31(13):3345-8. PMID: 12824323 [PubMed - indexed for MEDLINE] 9443: Stark A, Russell RB. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res. 2003 Jul 1;31(13):3341-4. PMID: 12824322 [PubMed - indexed for MEDLINE]
LOC3D: annotate sub-cellular localization for protein structures. Nucleic Acids Res. 2003 Jul 1;31(13):3337-40. PMID: 12824321 [PubMed - indexed for MEDLINE] 9445: Gaulton A, Attwood TK. Motif3D: Relating protein sequence motifs to 3D structure. Nucleic Acids Res. 2003 Jul 1;31(13):3333-6. PMID: 12824320 [PubMed - indexed for MEDLINE] 9446: Bennett SP, Lu L, Brutlag DL. 3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs. Nucleic Acids Res. 2003 Jul 1;31(13):3328-32. PMID: 12824319 [PubMed - indexed for MEDLINE]
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Download 12.14 Mb. Share with your friends:
|