Gene homology resources on the World Wide Web

Boston Children's Hospital, Boston, Massachusetts, United States
Physiological Genomics (Impact Factor: 2.37). 01/2003; 11(3):165-77. DOI: 10.1152/physiolgenomics.00112.2002
Source: PubMed


As the amount of information available to biologists increases exponentially, data analysis becomes progressively more challenging. Sequence homology has been a traditional tool in the researchers' armamentarium; it is a very versatile instrument and can be employed to assist in numerous tasks, from establishing the function of a gene to determination of the evolutionary development of an organism. Consequently, numerous specialized tools have been established in the public domain (most commonly, the World Wide Web) to help investigators use sequence homology in their research. These homology databases differ both in techniques they use to compare sequences as well as in the size of the unit of analysis, which can be the whole gene, a domain, or a motif. In this paper, we aim to present a systematic review of the inner details of the most commonly used databases as well as to offer guidelines for their use.

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    • "By 262 using data collected from various mouse and human transcriptome sources, Feldmesser et al. (2006) have 263 recently demonstrated that olfactory genes are widely expressed in such diverse organs as testis, kidney and 264 spermatozoa. It should be recalled at this juncture that homologous gene expression is experimentally 265 established through base sequence comparison (Turchin and Kohane, 2002), which indicates, therefore, that 266 homologous genes are not necessarily functionally equivalent, for they may come to realize different 267 functions in different tissues. The fact that olfactory genes were first identified in the olfactory epithelium 268 has placed some kind of historical legacy on them such that any subsequent functional attribution has been 269 conditioned by this initial interpretation. "
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    ABSTRACT: Any living organism interacts with and responds specifically to environmental molecules by expressing specific olfactory receptors. In this paper, this specificity will be first examined in causal terms with particular emphasis on the mechanisms controlling olfactory gene expression, cell-to-cell interactions and odor-decoding processes. However, this type of explanation does not entirely justify the role olfactory receptors have played during evolution, since they are also expressed ectopically in different organs and/or tissues. Homologous olfactory genes have in fact been found in such diverse cells and/or organs as spermatozoa, testis and kidney where they are assumed to act as chemotactic sensors or renin modulators. To justify their functional diversity, homologous olfactory receptors are assumed to share the same basic role: that of conferring a self-identity to cells or tissues under varying environmental conditions. By adopting this standpoint, the functional attribution as olfactory or chemotactic sensors to these receptors should not be seen either as a cause conditioning receptor gene expression, or as a final effect resulting from genetically predetermined programs, but as a direct consequence of the environmental conditions olfactory receptor genes have explored during evolution. The association of odorant patterns with specific environmental or contextual situations makes their relationship semiotically triadic, due to the emergence of an interpretant capable of perceiving odorants as meaningful signs out of a noisy background. This perspective highlights the importance of odorant-receptor relationships as respect to the properties of the interacting partners. It is our contention that only when taken together can these different explanatory strategies provide a realistic account of how olfactory receptor genes have been structurally and functionally modified during evolution.
    Biosemiotics 12/2011; 4(3). DOI:10.1007/s12304-011-9113-5 · 0.59 Impact Factor
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    • "The first step in such a comparison is the identification of putative orthologues of stress signalling molecules in these fungal genomes. This approach has been used effectively to assign provisional functional annotations to protein coding genes identified by genome sequencing [42-44], to measure the effects of functional genomic variables on protein evolution rates [45-47], and applied to other areas of evolutionary genomics [48], thereby increasing our understanding of eukaryotic evolution [49,50]. "
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    ABSTRACT: Microbes must sense environmental stresses, transduce these signals and mount protective responses to survive in hostile environments. In this study we have tested the hypothesis that fungal stress signalling pathways have evolved rapidly in a niche-specific fashion that is independent of phylogeny. To test this hypothesis we have compared the conservation of stress signalling molecules in diverse fungal species with their stress resistance. These fungi, which include ascomycetes, basidiomycetes and microsporidia, occupy highly divergent niches from saline environments to plant or mammalian hosts. The fungi displayed significant variation in their resistance to osmotic (NaCl and sorbitol), oxidative (H2O2 and menadione) and cell wall stresses (Calcofluor White and Congo Red). There was no strict correlation between fungal phylogeny and stress resistance. Rather, the human pathogens tended to be more resistant to all three types of stress, an exception being the sensitivity of Candida albicans to the cell wall stress, Calcofluor White. In contrast, the plant pathogens were relatively sensitive to oxidative stress. The degree of conservation of osmotic, oxidative and cell wall stress signalling pathways amongst the eighteen fungal species was examined. Putative orthologues of functionally defined signalling components in Saccharomyces cerevisiae were identified by performing reciprocal BLASTP searches, and the percent amino acid identities of these orthologues recorded. This revealed that in general, central components of the osmotic, oxidative and cell wall stress signalling pathways are relatively well conserved, whereas the sensors lying upstream and transcriptional regulators lying downstream of these modules have diverged significantly. There was no obvious correlation between the degree of conservation of stress signalling pathways and the resistance of a particular fungus to the corresponding stress. Our data are consistent with the hypothesis that fungal stress signalling components have undergone rapid recent evolution to tune the stress responses in a niche-specific fashion.
    BMC Evolutionary Biology 03/2009; 9(1):44. DOI:10.1186/1471-2148-9-44 · 3.37 Impact Factor
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    • "Search algorithms achieve the identifi cation by mapping the MS-derived peptide information to the applied database(s). Uncertain functional assignments of identifi ed proteins can be re-assessed by web-based tools for homology searches [Turchin and Kohane, 2002]. For identifi cation with PMF, experimentally (MS) determined masses are mapped to the calculated masses of theoretical peptides generated by an in silico tryptic digest of each protein entry in the used sequence database(s). "
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    ABSTRACT: The rapidly developing proteomics technologies help to advance the global understanding of physiological and cellular processes. The lifestyle of a study organism determines the type and complexity of a given proteomic project. The complexity of this study is characterized by a broad collection of pathway-specific subproteomes, reflecting the metabolic versatility as well as the regulatory potential of the aromatic-degrading, denitrifying bacterium 'Aromatoleum' sp. strain EbN1. Differences in protein profiles were determined using a gel-based approach. Protein identification was based on a progressive application of MALDI-TOF-MS, MALDI-TOF-MS/MS and LC-ESI-MS/MS. This progression was result-driven and automated by software control. The identification rate was increased by the assembly of a project-specific list of background signals that was used for internal calibration of the MS spectra, and by the combination of two search engines using a dedicated MetaScoring algorithm. In total, intelligent bioinformatics could increase the identification yield from 53 to 70% of the analyzed 5,050 gel spots; a total of 556 different proteins were identified. MS identification was highly reproducible: most proteins were identified more than twice from parallel 2DE gels with an average sequence coverage of >50% and rather restrictive score thresholds (Mascot >or=95, ProFound >or=2.2, MetaScore >or=97). The MS technologies and bioinformatics tools that were implemented and integrated to handle this complex proteomic project are presented. In addition, we describe the basic principles and current developments of the applied technologies and provide an overview over the current state of microbial proteome research.
    Journal of Molecular Microbiology and Biotechnology 02/2006; 11(1-2):53-81. DOI:10.1159/000092819 · 2.10 Impact Factor
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