Gene homology resources on the World Wide Web

Boston Children's Hospital, Boston, Massachusetts, United States
Physiological Genomics (Impact Factor: 2.81). 01/2003; 11(3):165-77. DOI: 10.1152/physiolgenomics.00112.2002
Source: PubMed

ABSTRACT 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.

  • Source
    • "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. "
    [Show abstract] [Hide abstract]
    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 · 0.49 Impact Factor
  • Source
    • "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). "
    [Show abstract] [Hide abstract]
    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 · 1.49 Impact Factor
  • Source
    • "Alignment of the predicted protein sequence of hephaestin with the functionally-similar protein Cp has revealed that the cDNA encoded a protein that is 50% identical to the mouse Cp (Vulpe et al. 1999). Guidelines relating to the use of databases may be obtained from, for example, Nadeau & Dunn (1998), Claverie (1999) and Turchin & Kohane (2002). "
    [Show abstract] [Hide abstract]
    ABSTRACT: As the 21st century moves forward, it is becoming more and more apparent that the genetic makeup of any individual strongly influences the way they metabolise nutrients. It is very important, therefore, to understand the techniques and technologies used to assess the contribution genes make to the physiology of an individual. Clearly, it is not possible to provide a comprehensive overview, but in the present review an attempt will be made to show, using examples from the authors' research, how these methods have contributed to this understanding. Studies are being undertaken into Fe transport across the placenta, from the mother to the fetus, and the consequences of maternal anaemia on pregnancy outcome. Levels of gene transcript and protein have been measured using Northern and Western blotting respectively. During the course of this work a new protein has been identified using the available human genome database. Following this 'in silico' or 'cyber biology', techniques such as real-time RT-PCR and RNA interference have been used to examine expression of this gene and its protein. The methods used, briefly how they work and some of their limitations will be explained. The objective of the present review is primarily to give a better perception of how molecular biology can be used in research and to help gain a clearer understanding of some of the techniques used.
    Proceedings of The Nutrition Society 09/2004; 63(3):481-90. DOI:10.1079/PNS2004368 · 4.94 Impact Factor
Show more