{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T08:37:07Z","timestamp":1771922227980,"version":"3.50.1"},"reference-count":15,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>With the ever-increasing number of gene sequences in the public databases, generating and analyzing multiple sequence alignments becomes increasingly time consuming. Nevertheless it is a task performed on a regular basis by researchers in many labs.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have now created a database called CoSMoS to find the occurrences and at the same time evaluate the significance of sequence motifs and amino acids encoded in the whole genome of the model organism <jats:italic>Escherichia coli<\/jats:italic> K12. We provide a precomputed set of multiple sequence alignments for each individual <jats:italic>E. coli<\/jats:italic> protein with all of its homologues in the RefSeq database. The alignments themselves, information about the occurrence of sequence motifs together with information on the conservation of each of the more than 1.3 million amino acids encoded in the <jats:italic>E. coli<\/jats:italic> genome can be accessed via the web interface of CoSMoS.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>CoSMoS is a valuable tool to identify highly conserved sequence motifs, to find regions suitable for mutational studies in functional analyses and to predict important structural features in <jats:italic>E. coli<\/jats:italic> proteins.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-37","type":"journal-article","created":{"date-parts":[[2006,1,27]],"date-time":"2006-01-27T19:15:35Z","timestamp":1138389335000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["CoSMoS: Conserved Sequence Motif Search in the proteome"],"prefix":"10.1186","volume":"7","author":[{"given":"Xiao I","family":"Liu","sequence":"first","affiliation":[]},{"given":"Neeraj","family":"Korde","sequence":"additional","affiliation":[]},{"given":"Ursula","family":"Jakob","sequence":"additional","affiliation":[]},{"given":"Lars I","family":"Leichert","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,1,24]]},"reference":[{"key":"776_CR1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4757-3783-7","volume-title":"Sequence-Evolution-Function: Computational Approaches in Comparative Genomics","author":"EV Koonin","year":"2003","unstructured":"Koonin EV, Galperin MY: Sequence-Evolution-Function: Computational Approaches in Comparative Genomics. Norwell, MA, Kluwer Academic Publishers; 2003."},{"issue":"3","key":"776_CR2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403\u2013410. 10.1006\/jmbi.1990.9999","journal-title":"J Mol Biol"},{"issue":"Web Server issu","key":"776_CR3","doi-asserted-by":"publisher","first-page":"W20","DOI":"10.1093\/nar\/gkh435","volume":"32","author":"S McGinnis","year":"2004","unstructured":"McGinnis S, Madden TL: BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004, 32(Web Server issue):W20\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"776_CR4","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1038\/scientificamerican1179-98","volume":"241","author":"M Kimura","year":"1979","unstructured":"Kimura M: The neutral theory of molecular evolution. Sci Am 1979, 241(5):98\u2013100, 102, 108 passim.","journal-title":"Sci Am"},{"issue":"1","key":"776_CR5","first-page":"1","volume":"5","author":"TC Hodgman","year":"1989","unstructured":"Hodgman TC: The elucidation of protein function by sequence motif analysis. Comput Appl Biosci 1989, 5(1):1\u201313.","journal-title":"Comput Appl Biosci"},{"issue":"14","key":"776_CR6","doi-asserted-by":"publisher","first-page":"5509","DOI":"10.1073\/pnas.87.14.5509","volume":"87","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Lipman DJ: Protein database searches for multiple alignments. 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Nucleic Acids Res 2004, 32(5):1792\u20131797. 10.1093\/nar\/gkh340","journal-title":"Nucleic Acids Res"},{"key":"776_CR9","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/1471-2105-5-113","volume":"5","author":"RC Edgar","year":"2004","unstructured":"Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5: 113. 10.1186\/1471-2105-5-113","journal-title":"BMC Bioinformatics"},{"key":"776_CR10","unstructured":"CoSMoS database download[http:\/\/www.biology.lsa.umich.edu\/cosmos\/files\/cosmos2.sql.bz2]"},{"key":"776_CR11","unstructured":"CoSMoS[http:\/\/www.biology.lsa.umich.edu\/cosmos]"},{"issue":"1","key":"776_CR12","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1093\/nar\/29.1.202","volume":"29","author":"JY Huang","year":"2001","unstructured":"Huang JY, Brutlag DL: The EMOTIF database. Nucleic Acids Res 2001, 29(1):202\u2013204. 10.1093\/nar\/29.1.202","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"776_CR13","first-page":"107","volume":"1","author":"A Gattiker","year":"2002","unstructured":"Gattiker A, Gasteiger E, Bairoch A: ScanProsite: a reference implementation of a PROSITE scanning tool. Appl Bioinformatics 2002, 1(2):107\u2013108.","journal-title":"Appl Bioinformatics"},{"key":"776_CR14","first-page":"28","volume":"2","author":"TL Bailey","year":"1994","unstructured":"Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2: 28\u201336.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"776_CR15","unstructured":"CoSMoS Protein Info[http:\/\/www.biology.lsa.umich.edu\/cosmos\/protein_info.php]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-37.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:04:55Z","timestamp":1630494295000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-37"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,1,24]]},"references-count":15,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["776"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-37","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,1,24]]},"assertion":[{"value":"7 September 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 January 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 January 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"37"}}