Nucleic Acids Research, 2000, Vol. 28, No. 1 228-230
© 2000 Oxford University Press
Increased coverage of protein families with the Blocks Database servers
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
Received September 29, 1999; Accepted October 4, 1999.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONBlocks+IMPROVED Block SEARCHER E-VALUESIMPALA SEARCHERMAPPING Blocks ONTO 3D...ACCESSREFERENCES |
|---|
The Blocks Database WWW (http://blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org ) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Blocks+ nearly doubles the number of protein families included in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PROSITE and PRINTS. Other new features include improved Block Searcher statistics, searching with NCBI’s IMPALA program and 3D display of blocks on PDB structures.
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONBlocks+IMPROVED Block SEARCHER E-VALUESIMPALA SEARCHERMAPPING Blocks ONTO 3D...ACCESSREFERENCES |
|---|
Blocks are ungapped multiple alignments corresponding to the most conserved regions of proteins. The Blocks Database consists of blocks constructed from documented families of related proteins using the automated PROTOMAT system (1). In addition to searching the Blocks Database for sequence similarities, several enhancements have been introduced for exploiting protein family information implicit in blocks (2). These include blocks-based searching of sequence databanks (3), blocks-versus-blocks searching (4), sequence logo and tree representations of multiple alignments, and PCR primer design using the CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) method (5). During the past year, coverage of the default Blocks Database has increased with the addition of families from several compendiums, and new Blocks Database searching and 3D display options have been implemented.
|
Blocks+ |
|---|
|
TOPABSTRACTINTRODUCTIONBlocks+IMPROVED Block SEARCHER E-VALUESIMPALA SEARCHERMAPPING Blocks ONTO 3D...ACCESSREFERENCES |
|---|
Previously, lists of protein families for the Blocks Database were obtained from the PROSITE catalog (6) and supplemented with additional families from the PRINTS database (7). Now, additional families are obtained from the Pfam-A (8), ProDom (9) and Domo (10) protein family databases. Blocks for these famililes are computed by extracting SWISS-PROT (11) sequences documented in the source protein family databases and presenting them to the automated PROTOMAT system (1). However, to minimize redundancy, the resulting blocks for a family are added to Blocks+ only if a LAMA blocks-versus-blocks search (4) of them against the current database results in no significant hits. This recursive procedure yields sets of blocks extracted from Pfam-A families not found in either PROSITE or PRINTS, blocks from ProDom not found in the previous three databases and blocks from Domo not found in any of the other databases. The Blocks+ Database (12) represents 9498 blocks from 2129 different protein families as of June 15, 1999 (Fig. 1). Since the multiple alignments in the source family databases are not used, the alignments in Blocks+ may not coincide with them. Therefore, LAMA is used to search each set of blocks in Blocks+ against blocks carved out of these source alignments (2), and WWW links are made when hits are found.
|
The Blocks WWW and Email servers provide tools to search DNA and protein queries against Blocks+. As an option to avoid false positive hits, a subset of Blocks+ from which many compositionally biased blocks have been removed can be searched. The Blocks+ Database can also be queried with key words or with blocks or other multiple alignments using the multiple alignment processor and the LAMA search engine. All search results are linked to corresponding entries in the Blocks+ Database which include phylogenetic trees, sequence logos and 3D structures, plus links to other sequence and protein family databases.
|
IMPROVED Block SEARCHER E-VALUES |
|---|
|
TOPABSTRACTINTRODUCTIONBlocks+IMPROVED Block SEARCHER E-VALUESIMPALA SEARCHERMAPPING Blocks ONTO 3D...ACCESSREFERENCES |
|---|
The Block Searcher uses the BLIMPS searching program (13) to compare a DNA or protein query sequence with each block in the database of blocks being searched. The results for individual blocks are then analyzed to combine hits for blocks belonging to the same protein family. The original analysis program, BLKSORT, computes E-values for a hit to a family based on ranks (14). A new analysis program, BLKPROB, computes E-values for multiple block hits using methods developed for searches of block queries against sequence databases with the MAST searching tool (15,16). This method requires computing the score distribution for each block, which can be done explicitly when the position-specific scoring matrix (PSSM) derived from a block contains only integers (17). The probability of obtaining the score for the alignment with the query sequence can then simply be looked up in the score distribution. The current implementation computes the complete distributions only for blocks that attain a score greater than the 99.5th percentile score of the distribution; this value is pre-computed and stored with each block. An example of the new output appears in Figure 2a.
|
The original analysis program with E-values based on ranks is still available as an option and remains the default for the Blocks Email Searcher (to maintain a standardized format for high-volume automatic submissions). However, Email users are encouraged to try the improved analysis program; the required message format is described at http://blocks.fhcrc.org/help/email.html
|
IMPALA SEARCHER |
|---|
|
TOPABSTRACTINTRODUCTIONBlocks+IMPROVED Block SEARCHER E-VALUESIMPALA SEARCHERMAPPING Blocks ONTO 3D...ACCESSREFERENCES |
|---|
A new alternative to the Block Searcher for protein queries is the IMPALA Searcher, which has been made available for the Blocks WWW server by the BLAST group at NCBI (18). IMPALA searches a suitably formatted database of PSI-BLAST PSSMs (19). These are constructed for each family in Blocks+ by PSI-BLAST searching with the COBBLER (COnsensus Biasing By Locally Embedding Residues) sequence (3) as query against the SWISS-PROT sequences known to belong to the family. The COBBLER sequence is a representative sequence stretching from 10 aa upstream of the first block to 10 aa downstream of the last block, into which consensus residues deduced from block regions are embedded. PSI-BLAST searching is iterated until convergence, yielding a database of one PSI-BLAST PSSM for each family in Blocks+. Figure 2b shows an example of IMPALA output, which consists of the familiar BLAST output and E-value statistics, and includes links to the Blocks+ families hit. Unlike the Block Searcher, IMPALA may insert gaps in the alignment of the query with the blocks and may also align regions between blocks. Since the Blocks and IMPALA Searchers tend to report the same true positive hits but different false positives (e.g. compare Fig. 2a with b), users who search with both and compare the results may be able to better distinguish true from false hits for challenging queries.
|
MAPPING Blocks ONTO 3D STRUCTURES |
|---|
|
TOPABSTRACTINTRODUCTIONBlocks+IMPROVED Block SEARCHER E-VALUESIMPALA SEARCHERMAPPING Blocks ONTO 3D...ACCESSREFERENCES |
|---|
An increasing number of protein families are represented by one or more 3D structures in the PDB database (http://www.rcsb.org/pdb ). To map blocks onto a structure in PDB, MAST (15) is used to search PSSMs against the database of PDB sequences. Segments within corresponding PDB structures are color-coded to indicate the block that they represent. The 3D Blocks representation can be viewed by WWW browsers with helper software that can process Rasmol (20) commands, such as Chime (http://www.mdl.com/chemscape/chime ).
|
ACCESS |
|---|
|
TOPABSTRACTINTRODUCTIONBlocks+IMPROVED Block SEARCHER E-VALUESIMPALA SEARCHERMAPPING Blocks ONTO 3D...ACCESSREFERENCES |
|---|
The Blocks WWW server at http://blocks.fhcrc.org implements all of the features described in this article, which should be cited when the Blocks server is used. The Blocks+ Database can also be searched via Email by sending a DNA or protein sequence in FASTA format to blocks@blocks.fhcrc.org
|
ACKNOWLEDGEMENTS |
|---|
We thank Nick Taylor for implementating 3D Blocks and the NCBI BLAST group, especially Alejandro Schaffer, for making IMPALA software available for searching the Blocks Database. This work is supported by grants from the NIH (GM29009) and the DOE (DE-FG03-97ER62382).
|
FOOTNOTES |
|---|
* To whom correspondence should be addressed. Tel: +1 206 667 4515; Fax: +1 206 667 5889; Email: steveh@fhcrc.org Present address: Shmuel Pietrokovski, The Weizmann Institute, Rehovot 76100, Israel
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONBlocks+IMPROVED Block SEARCHER E-VALUESIMPALA SEARCHERMAPPING Blocks ONTO 3D...ACCESSREFERENCES |
|---|
-
1 Henikoff,S. and Henikoff,J.G. (1991) Nucleic Acids Res., 19, 6565–6572.
2 Henikoff,J.G., Henikoff,S. and Pietrokovski,S. (1999) Nucleic Acids Res., 27, 226–228.
3 Henikoff,S. and Henikoff,J.G. (1997) Protein Sci., 6, 698–705.[Web of Science][Medline]
4 Pietrokovski,S. (1996) Nucleic Acids Res., 24, 3836–3845.
5 Rose,T.M., Schultz,E.R., Henikoff,J.G., Pietrokovski,S., McCallum,C.M. and Henikoff,S. (1998) Nucleic Acids Res., 26, 1628–1635.
6 Hofmann,K., Bucher,P., Falquet,L. and Bairoch,A. (1999) Nucleic Acids Res., 27, 215–219.
7 Attwood,T.K., Flower,D.R., Lewis,A.P., Mabey,J.E., Morgan,S.R., Scordis,P., Selley,J.N. and Wright,W. (1999) Nucleic Acids Res., 27, 220–225.
8 Bateman,A., Birney,E., Durbin,R., Eddy,S.R., Finn,R.D. and Sonnhammer,E.L.L. (1999) Nucleic Acids Res., 27, 260–262. Updated article in this issue: Nucleic Acids Res. (2000), 28, 225–227.
9 Corpet,F., Gouzy,J. and Kahn,D. (1999) Nucleic Acids Res., 27, 263–267. Updated article in this issue: Nucleic Acids Res. (2000), 28, 267–269.
10 Gracy,J. and Argos,P. (1998) Bioinformatics, 14, 164–173.
11 Bairoch,A. and Boeckmann,B. (1992) Nucleic Acids Res., 20, 2019–2022.
12 Henikoff,S., Henikoff,J.G. and Pietrokovski,S. (1999) Bioinformatics, 15, 471–479.
13 Henikoff,S., Henikoff,J.G., Alford,W.J. and Pietrokovski,S. (1995) Gene, 163, GC17–GC26.[Medline]
14 Henikoff,S. and Henikoff,J.G. (1994) Genomics, 19, 97–107.[Web of Science][Medline]
15 Bailey,T.L. and Gribskov,M. (1997) J. Comput. Biol., 4, 45–59.[Web of Science][Medline]
16 Bailey,T.L. and Gribskov,M. (1998) Bioinformatics, 14, 48–54.
17 Tatusov,R.L., Altschul,S.F. and Koonin,E.V. (1994) Proc. Natl Acad. Sci. USA, 91, 12091–12095.
18 Schaffer,A.A., Wolf,Y.I., Ponting,C.P., Koonin,E.V., Aravind,L. and Altschul,S.F. (1999) Bioinformatics, in press.
19 Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389–3402.
20 Sayle,R.A. and Milner-White,E.F. (1995) Trends Biochem. Sci., 20, 374.[Web of Science][Medline]
21 Henikoff,S. and Comai,L. (1998) Genetics, 149, 307–318.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. H. Fong and A. Marchler-Bauer CORAL: aligning conserved core regions across domain families Bioinformatics, August 1, 2009; 25(15): 1862 - 1868. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. T.-H. Chang, T.-Y. Chien, and C.-Y. Chen seeMotif: exploring and visualizing sequence motifs in 3D structures Nucleic Acids Res., July 1, 2009; 37(suppl_2): W552 - W558. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Rajasekaran, S. Balla, P. Gradie, M. R. Gryk, K. Kadaveru, V. Kundeti, M. W. Maciejewski, T. Mi, N. Rubino, J. Vyas, et al. Minimotif miner 2nd release: a database and web system for motif search Nucleic Acids Res., January 1, 2009; 37(suppl_1): D185 - D190. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K.-R. Chung and H.-L. Liao Determination of a transcriptional regulator-like gene involved in biosynthesis of elsinochrome phytotoxin by the citrus scab fungus, Elsinoe fawcettii Microbiology, November 1, 2008; 154(11): 3556 - 3566. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ye, G. Vriend, and A. P. IJzerman Tracing evolutionary pressure Bioinformatics, April 1, 2008; 24(7): 908 - 915. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Palmeri, S. Spadavecchia, K. D. Carroll, and D. M. Lukac Promoter- and Cell-Specific Transcriptional Transactivation by the Kaposi's Sarcoma-Associated Herpesvirus ORF57/Mta Protein J. Virol., December 15, 2007; 81(24): 13299 - 13314. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Sulakhe, M. D'Souza, M. Syed, A. Rodriguez, Y. Zhang, E. M. Glass, M. F. Romine, and N. Maltsev GNARE--a grid-based server for the analysis of user submitted genomes Nucleic Acids Res., May 25, 2007; (2007) gkm366v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Przybylski and B. Rost Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments Nucleic Acids Res., April 1, 2007; 35(7): 2238 - 2246. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Sun and J. Buhler Designing patterns for profile HMM search Bioinformatics, January 15, 2007; 23(2): e36 - e43. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. D'Souza, E. M. Glass, M. H. Syed, Y. Zhang, A. Rodriguez, N. Maltsev, and M. Y. Galperin Sentra: a database of signal transduction proteins for comparative genome analysis Nucleic Acids Res., January 12, 2007; 35(suppl_1): D271 - D273. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Tian, J. Win, J. Song, R. van der Hoorn, E. van der Knaap, and S. Kamoun A Phytophthora infestans Cystatin-Like Protein Targets a Novel Tomato Papain-Like Apoplastic Protease Plant Physiology, January 1, 2007; 143(1): 364 - 377. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Friedberg Automated protein function prediction--the genomic challenge Brief Bioinform, September 1, 2006; 7(3): 225 - 242. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Kuwae, T. Matsuzawa, N. Ishikawa, H. Abe, T. Nonaka, H. Fukuda, S. Imajoh-Ohmi, and A. Abe BopC Is a Novel Type III Effector Secreted by Bordetella bronchiseptica and Has a Critical Role in Type III-dependent Necrotic Cell Death J. Biol. Chem., March 10, 2006; 281(10): 6589 - 6600. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Mullan Pairwise sequence alignment--it's all about us! Brief Bioinform, March 1, 2006; 7(1): 113 - 115. [Full Text] [PDF]
|
|
|
|
 |
|
 P. Hudson, T. S. Gorton, L. Papazisi, K. Cecchini, S. Frasca Jr., and S. J. Geary Identification of a Virulence-Associated Determinant, Dihydrolipoamide Dehydrogenase (lpd), in Mycoplasma gallisepticum through In Vivo Screening of Transposon Mutants Infect. Immun., February 1, 2006; 74(2): 931 - 939. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. A. Price, G. E. Crooks, R. E. Green, and S. E. Brenner Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap Bioinformatics, October 15, 2005; 21(20): 3824 - 3831. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. E. Crooks, R. E. Green, and S. E. Brenner Pairwise alignment incorporating dipeptide covariation Bioinformatics, October 1, 2005; 21(19): 3704 - 3710. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Frenkel-Morgenstern, A. Singer, H. Bronfeld, and S. Pietrokovski One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries Nucleic Acids Res., July 1, 2005; 33(suppl_2): W281 - W283. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Wang and R. Samudrala FSSA: a novel method for identifying functional signatures from structural alignments Bioinformatics, July 1, 2005; 21(13): 2969 - 2977. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Weiner 3rd, G. Thomas, and E. Bornberg-Bauer Rapid motif-based prediction of circular permutations in multi-domain proteins Bioinformatics, April 1, 2005; 21(7): 932 - 937. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. E. Crooks and S. E. Brenner An alternative model of amino acid replacement Bioinformatics, April 1, 2005; 21(7): 975 - 980. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Shiba, H. Itoh, A. Kameda, K. Kobayashi, Y. Kawazoe, and T. Noguchi Polyphosphate:AMP Phosphotransferase as a Polyphosphate-Dependent Nucleoside Monophosphate Kinase in Acinetobacter johnsonii 210A J. Bacteriol., March 1, 2005; 187(5): 1859 - 1865. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Liu, J. I. B. Bos, M. Armstrong, S. C. Whisson, L. da Cunha, T. Torto-Alalibo, J. Win, A. O. Avrova, F. Wright, P. R. J. Birch, et al. Patterns of Diversifying Selection in the Phytotoxin-like scr74 Gene Family of Phytophthora infestans Mol. Biol. Evol., March 1, 2005; 22(3): 659 - 672. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. J. Su, L. Lu, S. Saxonov, and D. L. Brutlag eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity Nucleic Acids Res., January 1, 2005; 33(suppl_1): D178 - D182. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Abhiman and E. L. L. Sonnhammer FunShift: a database of function shift analysis on protein subfamilies Nucleic Acids Res., January 1, 2005; 33(suppl_1): D197 - D200. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. D. Gonzales, E. Archuleta, A. Farmer, K. Gajendran, D. Grant, R. Shoemaker, W. D. Beavis, and M. E. Waugh The Legume Information System (LIS): an integrated information resource for comparative legume biology Nucleic Acids Res., January 1, 2005; 33(suppl_1): D660 - D665. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Tian, A. K. Arakaki, and J. Skolnick EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference Nucleic Acids Res., December 1, 2004; 32(21): 6226 - 6239. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. K. Papasaikas, P. G. Bagos, Z. I. Litou, V. J. Promponas, and S. J. Hamodrakas PRED-GPCR: GPCR recognition and family classification server Nucleic Acids Res., July 1, 2004; 32(suppl_2): W380 - W382. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Maudling and T. K. Attwood FAN: fingerprint analysis of nucleotide sequences Nucleic Acids Res., July 1, 2004; 32(suppl_2): W620 - W623. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Tian, E. Huitema, L. da Cunha, T. Torto-Alalibo, and S. Kamoun A Kazal-like Extracellular Serine Protease Inhibitor from Phytophthora infestans Targets the Tomato Pathogenesis-related Protease P69B J. Biol. Chem., June 18, 2004; 279(25): 26370 - 26377. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Y. Lau and D. I. Chasman Functional classification of proteins and protein variants PNAS, April 27, 2004; 101(17): 6576 - 6581. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Thompson, V. Prigent, and O. Poch LEON: multiple aLignment Evaluation Of Neighbours Nucleic Acids Res., February 24, 2004; 32(4): 1298 - 1307. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Gaulton and T. K. Attwood Motif3D: relating protein sequence motifs to 3D structure Nucleic Acids Res., July 1, 2003; 31(13): 3333 - 3336. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Puntervoll, R. Linding, C. Gemund, S. Chabanis-Davidson, M. Mattingsdal, S. Cameron, D. M. A. Martin, G. Ausiello, B. Brannetti, A. Costantini, et al. ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins Nucleic Acids Res., July 1, 2003; 31(13): 3625 - 3630. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. McDermott and R. Samudrala Bioverse: functional, structural and contextual annotation of proteins and proteomes Nucleic Acids Res., July 1, 2003; 31(13): 3736 - 3737. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. E. Taylor and E. A. Greene PARSESNP: a tool for the analysis of nucleotide polymorphisms Nucleic Acids Res., July 1, 2003; 31(13): 3808 - 3811. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. JACKMAN, R. K. MONTANGE, H. S. MALIK, and E. M. PHIZICKY Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9 RNA, May 1, 2003; 9(5): 574 - 585. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. J. Till, S. H. Reynolds, E. A. Greene, C. A. Codomo, L. C. Enns, J. E. Johnson, C. Burtner, A. R. Odden, K. Young, N. E. Taylor, et al. Large-Scale Discovery of Induced Point Mutations With High-Throughput TILLING Genome Res., March 1, 2003; 13(3): 524 - 530. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. C. Schuyler, J. Y. Liu, and D. Pellman The molecular function of Ase1p: evidence for a MAP-dependent midzone-specific spindle matrix J. Cell Biol., February 18, 2003; 160(4): 517 - 528. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. R. Panchenko Finding weak similarities between proteins by sequence profile comparison Nucleic Acids Res., January 15, 2003; 31(2): 683 - 689. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Liu, A. E. Loraine, R. Shigeta, M. Cline, J. Cheng, V. Valmeekam, S. Sun, D. Kulp, and M. A. Siani-Rose NetAffx: Affymetrix probesets and annotations Nucleic Acids Res., January 1, 2003; 31(1): 82 - 86. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. K. Attwood, P. Bradley, D. R. Flower, A. Gaulton, N. Maudling, A. L. Mitchell, G. Moulton, A. Nordle, K. Paine, P. Taylor, et al. PRINTS and its automatic supplement, prePRINTS Nucleic Acids Res., January 1, 2003; 31(1): 400 - 402. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Turchin and I. S. Kohane Gene homology resources on the World Wide Web Physiol Genomics, December 3, 2002; 11(3): 165 - 177. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Saitoh, S. Miyagi, H. Ariga, and K.-i. Tsutsumi Functional domains involved in the interaction between Orc1 and transcriptional repressor AlF-C that bind to an origin/promoter of the rat aldolase B gene Nucleic Acids Res., December 1, 2002; 30(23): 5205 - 5212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Schug, S. Diskin, J. Mazzarelli, B. P. Brunk, and C. J. Stoeckert Jr. Predicting Gene Ontology Functions from ProDom and CDD Protein Domains Genome Res., April 1, 2002; 12(4): 648 - 655. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Peterbauer, J. Mucha, L. Mach, and A. Richter Chain Elongation of Raffinose in Pea Seeds. ISOLATION, CHARCTERIZATION, AND MOLECULAR CLONING OF A MULTIFUNCTIONAL ENZYME CATALYZING THE SYNTHESIS OF STACHYOSE AND VERBASCOSE J. Biol. Chem., January 4, 2002; 277(1): 194 - 200. [Abstract] [Full Text]
|
|
|
|
|
|
T. K. Attwood, M. J. Blythe, D. R. Flower, A. Gaulton, J. E. Mabey, N. Maudling, L. McGregor, A. L. Mitchell, G. Moulton, K. Paine, et al. PRINTS and PRINTS-S shed light on protein ancestry Nucleic Acids Res., January 1, 2002; 30(1): 239 - 241. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Maltsev, E. Marland, G. X. Yu, S. Bhatnagar, and R. Lusk Sentra, a database of signal transduction proteins Nucleic Acids Res., January 1, 2002; 30(1): 349 - 350. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T.K. Attwood, M.D.R. Croning, and A. Gaulton Deriving structural and functional insights from a ligand-based hierarchical classification of G protein-coupled receptors Protein Eng. Des. Sel., January 1, 2002; 15(1): 7 - 12. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Murvai, K. Vlahovicek, C. Szepesvari, and S. Pongor Prediction of Protein Functional Domains from Sequences Using Artificial Neural Networks Genome Res., August 1, 2001; 11(8): 1410 - 1417. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Qian, B. Stenger, C. A. Wilson, J. Lin, R. Jansen, S. A. Teichmann, J. Park, W. G. Krebs, H. Yu, V. Alexandrov, et al. PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information Nucleic Acids Res., April 15, 2001; 29(8): 1750 - 1764. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M. D. R. Croning, et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites Nucleic Acids Res., January 1, 2001; 29(1): 37 - 40. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. H. Haft, B. J. Loftus, D. L. Richardson, F. Yang, J. A. Eisen, I. T. Paulsen, and O. White TIGRFAMs: a protein family resource for the functional identification of proteins Nucleic Acids Res., January 1, 2001; 29(1): 41 - 43. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. T. Silverstein, E. Shoop, J. E. Johnson, A. Kilian, J. L. Freeman, T. M. Kunau, I. A. Awad, M. Mayer, and E. F. Retzel The MetaFam Server: a comprehensive protein family resource Nucleic Acids Res., January 1, 2001; 29(1): 49 - 51. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. H. Wu, C. Xiao, Z. Hou, H. Huang, and W. C. Barker iProClass: an integrated, comprehensive and annotated protein classification database Nucleic Acids Res., January 1, 2001; 29(1): 52 - 54. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Murvai, K. Vlahovicek, E. Barta, and S. Pongor The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments Nucleic Acids Res., January 1, 2001; 29(1): 58 - 60. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Y. Huang and D. L. Brutlag The EMOTIF database Nucleic Acids Res., January 1, 2001; 29(1): 202 - 204. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. S. Malik, S. Henikoff, and T. H. Eickbush Poised for Contagion: Evolutionary Origins of the Infectious Abilities of Invertebrate Retroviruses Genome Res., September 1, 2000; 10(9): 1307 - 1318. [Abstract] [Full Text]
|
|
|
|
|
|
J. G. Henikoff and S. Henikoff Drosophila Genomic Sequence Annotation Using the BLOCKS+ Database Genome Res., April 1, 2000; 10(4): 543 - 546. [Abstract] [Full Text]
|
|
|
|
 |
|
 G. M. Rubin, M. D. Yandell, J. R. Wortman, G. L. Gabor Miklos, C. R. Nelson, I. K. Hariharan, M. E. Fortini, P. W. Li, R. Apweiler, W. Fleischmann, et al. Comparative Genomics of the Eukaryotes Science, March 24, 2000; 287(5461): 2204 - 2215. [Abstract] [Full Text]
|
|
|
|
|
|
S. Wiemann, B. Weil, R. Wellenreuther, J. Gassenhuber, S. Glassl, W. Ansorge, M. Böcher, H. Blöcker, S. Bauersachs, H. Blum, et al. Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs Genome Res., March 1, 2001; 11(3): 422 - 435. [Abstract] [Full Text]
|
|
|
|
|
|
J. H. Heaton, W. M. Dlakic, M. Dlakic, and T. D. Gelehrter Identification and cDNA Cloning of a Novel RNA-binding Protein That Interacts with the Cyclic Nucleotide-responsive Sequence in the Type-1 Plasminogen Activator Inhibitor mRNA J. Biol. Chem., January 26, 2001; 276(5): 3341 - 3347. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||