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  • 1
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    Altered growth and branching patterns in synpolydactyly caused by mutations in HOXD13 (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-04-26
    Description: Hox genes regulate patterning during limb development. It is believed that they function in the determination of the timing and extent of local growth rates. Here, it is demonstrated that synpolydactyly, an inherited human abnormality of the hands and feet, is caused by expansions of a polyalanine stretch in the amino-terminal region of HOXD13. The homozygous phenotype includes the transformation of metacarpal and metatarsal bones to short carpal- and tarsal-like bones. The mutations identify the polyalanine stretch outside of the DNA binding domain of HOXD13 as a region necessary for proper protein function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muragaki, Y -- Mundlos, S -- Upton, J -- Olsen, B R -- AR36819/AR/NIAMS NIH HHS/ -- AR36820/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Apr 26;272(5261):548-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8614804" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Chromosome Mapping ; Chromosomes, Human, Pair 2 ; Cloning, Molecular ; Female ; Fingers/*abnormalities/embryology ; *Genes, Homeobox ; Genetic Linkage ; Homeodomain Proteins/chemistry/*genetics/physiology ; Humans ; Male ; Molecular Sequence Data ; Morphogenesis ; Multigene Family ; Mutation ; Pedigree ; Peptides/chemistry ; Polydactyly/embryology/*genetics/radiography ; Polymerase Chain Reaction ; Syndactyly/embryology/*genetics/radiography ; Toes/*abnormalities/embryology ; *Transcription Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Lessons from an Archaeal genome: what are we learning from Methanococcus jannaschii? (1996)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: No abstract available
    Keywords: Exobiology
    Type: Trends in genetics : TIG (ISSN 0168-9525); Volume 12; 10; 377-9
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  • 3
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    Archaeal genomics: an overview (1997)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: No abstract available
    Keywords: Exobiology
    Type: Cell (ISSN 0092-8674); Volume 89; 7; 991-4
    Format: text
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  • 4
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    A new version of the RDP (Ribosomal Database Project) (1999)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include 〉9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.
    Keywords: Exobiology
    Type: Nucleic acids research (ISSN 0305-1048); Volume 27; 1; 171-3
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  • 5
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    Methanococcus jannaschii genome: revisited (1996)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: Analysis of genomic sequences is necessarily an ongoing process. Initial gene assignments tend (wisely) to be on the conservative side (Venter, 1996). The analysis of the genome then grows in an iterative fashion as additional data and more sophisticated algorithms are brought to bear on the data. The present report is an emendation of the original gene list of Methanococcus jannaschii (Bult et al., 1996). By using a somewhat more updated database and more relaxed (and operator-intensive) pattern matching methods, we were able to add significantly to, and in a few cases amend, the gene identification table originally published by Bult et al. (1996).
    Keywords: Exobiology
    Type: Microbial & comparative genomics (ISSN 1090-6592); Volume 1; 4; 329-38
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  • 6
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    Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species (1999)
    In:  Other Sources
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    Publication Date: 2019-07-13
    Description: The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs from mesophilic Methanococcus species. Although the growth temperatures of the mesophiles are about 50 degrees C below that of M. jannaschii, their genomic G+C contents are nearly identical. The properties most correlated with the proteins of the thermophile include higher residue volume, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and fewer uncharged polar residues (Ser, Thr, Asn, and Gln). These are recurring themes, with all trends applying to 83-92% of the proteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature change are the same relatively conservative changes observed in all proteins, but in the case of the mesophile/thermophile comparison there is a directional bias. We identify 26 specific pairs of amino acids with a statistically significant (P 〈 0.01) preferred direction of replacement.
    Keywords: Exobiology
    Type: Proceedings of the National Academy of Sciences of the United States of America (ISSN 0027-8424); 96; 7; 3578-83
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  • 7
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    CRITICA: coding region identification tool invoking comparative analysis (1999)
    In:  Other Sources
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    Publication Date: 2019-07-13
    Description: Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).
    Keywords: Exobiology
    Type: Molecular biology and evolution (ISSN 0737-4038); 16; 4; 512-24
    Format: text
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