Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Jan 1;24(1):210–213. doi: 10.1093/nar/24.1.210

The SBASE protein domain library, Release 4.0: a collection of annotated protein sequence segments.

J Murvai 1, A Gabrielian 1, P Fábián 1, Z Hátsagi 1, K Degtyarenko 1, H Hegyi 1, S Pongor 1
PMCID: PMC145610  PMID: 8594582

Abstract

SBASE 4.0 is the fourth release of SBASE, a collection of annotated protein domain sequences that represent various structural, functional, ligand binding and topogenic segments of proteins. SBASE was designed to facilitate the detection of functional homologies and can be searched with standard database search tools, such as FASTA and BLAST3. The present release contains 61 137 entries provided with standardized names and cross-referenced to all major protein, nucleic acid and sequence pattern collections. The entries are clustered into 13 155 groups in order to facilitate detection of distant similarities. SBASE 4.0 is freely available by anonymous ftp file transfer from ftp.icgeb.trieste.it. Individual records can be retrieved with the gopher server at icgeb.trieste.it and with a World Wide Web server at http://www.icgeb.trieste.it. Automated searching of SBASE with BLAST can be carried out with the electronic mail server sbase@icgeb.trieste.it, which now also provides a graphic representation of the homologies. A related mail server, domain@hubi.abc.hu, assigns SBASE domain homologies on the basis of SWISS-PROT searches.

Full Text

The Full Text of this article is available as a PDF (57.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Lipman D. J. Protein database searches for multiple alignments. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5509–5513. doi: 10.1073/pnas.87.14.5509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Appel R. D., Sanchez J. C., Bairoch A., Golaz O., Ravier F., Pasquali C., Hughes G. J., Hochstrasser D. F. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis. Nucleic Acids Res. 1994 Sep;22(17):3581–3582. [PMC free article] [PubMed] [Google Scholar]
  3. Attwood T. K., Beck M. E., Bleasby A. J., Parry-Smith D. J. PRINTS--a database of protein motif fingerprints. Nucleic Acids Res. 1994 Sep;22(17):3590–3596. [PMC free article] [PubMed] [Google Scholar]
  4. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res. 1994 Sep;22(17):3578–3580. [PMC free article] [PubMed] [Google Scholar]
  5. Bairoch A., Bucher P. PROSITE: recent developments. Nucleic Acids Res. 1994 Sep;22(17):3583–3589. [PMC free article] [PubMed] [Google Scholar]
  6. Barker W. C., Hunt L. T., George D. G. Identifying domains in protein sequences. Protein Seq Data Anal. 1988;1(5):363–373. [PubMed] [Google Scholar]
  7. Baron M., Norman D. G., Campbell I. D. Protein modules. Trends Biochem Sci. 1991 Jan;16(1):13–17. doi: 10.1016/0968-0004(91)90009-k. [DOI] [PubMed] [Google Scholar]
  8. Benson D. A., Boguski M., Lipman D. J., Ostell J. GenBank. Nucleic Acids Res. 1994 Sep;22(17):3441–3444. doi: 10.1093/nar/22.17.3441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  10. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Emmert D. B., Stoehr P. J., Stoesser G., Cameron G. N. The European Bioinformatics Institute (EBI) databases. Nucleic Acids Res. 1994 Sep;22(17):3445–3449. doi: 10.1093/nar/22.17.3445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. George D. G., Barker W. C., Mewes H. W., Pfeiffer F., Tsugita A. The PIR-International Protein Sequence Database. Nucleic Acids Res. 1994 Sep;22(17):3569–3573. [PMC free article] [PubMed] [Google Scholar]
  13. Ghosh D. Status of the transcription factors database (TFD). Nucleic Acids Res. 1993 Jul 1;21(13):3117–3118. doi: 10.1093/nar/21.13.3117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hegyi H., Pongor S. Predicting potential domain homologies from FASTA search results. Comput Appl Biosci. 1993 Jun;9(3):371–372. doi: 10.1093/bioinformatics/9.3.371. [DOI] [PubMed] [Google Scholar]
  15. Henikoff S., Henikoff J. G. Protein family classification based on searching a database of blocks. Genomics. 1994 Jan 1;19(1):97–107. doi: 10.1006/geno.1994.1018. [DOI] [PubMed] [Google Scholar]
  16. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  17. Pearson P., Francomano C., Foster P., Bocchini C., Li P., McKusick V. The status of online Mendelian inheritance in man (OMIM) medio 1994. Nucleic Acids Res. 1994 Sep;22(17):3470–3473. doi: 10.1093/nar/22.17.3470. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Pongor S., Hátsági Z., Degtyarenko K., Fábián P., Skerl V., Hegyi H., Murvai J., Bevilacqua V. The SBASE protein domain library, release 3.0: a collection of annotated protein sequence segments. Nucleic Acids Res. 1994 Sep;22(17):3610–3615. [PMC free article] [PubMed] [Google Scholar]
  19. Pongor S., Skerl V., Cserzö M., Hátsági Z., Simon G., Bevilacqua V. The SBASE domain library: a collection of annotated protein segments. Protein Eng. 1993 Jun;6(4):391–395. doi: 10.1093/protein/6.4.391. [DOI] [PubMed] [Google Scholar]
  20. Roberts R. J., Macelis D. REBASE--restriction enzymes and methylases. Nucleic Acids Res. 1994 Sep;22(17):3628–3639. doi: 10.1093/nar/22.17.3628. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sonnhammer E. L., Durbin R. A workbench for large-scale sequence homology analysis. Comput Appl Biosci. 1994 Jun;10(3):301–307. doi: 10.1093/bioinformatics/10.3.301. [DOI] [PubMed] [Google Scholar]
  22. Sonnhammer E. L., Kahn D. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 1994 Mar;3(3):482–492. doi: 10.1002/pro.5560030314. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES