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Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences.
We describe a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region andExpand
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Searching databases of conserved sequence regions by aligning protein multiple-alignments.
A general searching method for comparing multiple sequence alignments was developed to detect sequence relationships between conserved protein regions. Multiple alignments are treated as sequences ofExpand
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Increased coverage of protein families with the Blocks Database servers
The Blocks Database WWW (http://blocks.fhcrc.org ) and Email (blocks@blocks.org) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Expand
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Network analysis of protein structures identifies functional residues.
Identifying active site residues strictly from protein three-dimensional structure is a difficult task, especially for proteins that have few or no homologues. We transformed protein structures intoExpand
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Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations
We use five databases to construct Blocks+, a unified database that is built on the PROTOMAT/BLOSUM scoring model and that can be searched using a single algorithm for consistent sequence classification. Expand
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USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses
Usher syndrome type 3 (USH3) is an autosomal recessive disorder characterised by the association of post-lingual progressive hearing loss, progressive visual loss due to retinitis pigmentosa andExpand
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Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings.
I-TevI is a member of the GIY-YIG family of homing endonucleases. It is folded into two structural and functional domains, an N-terminal catalytic domain and a C-terminal DNA-binding domain,Expand
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Modular organization of inteins and C‐terminal autocatalytic domains
  • S. Pietrokovski
  • Medicine, Chemistry
  • Protein science : a publication of the Protein…
  • 1 January 1998
Analysis of the conserved sequence features of inteins (protein “introns”) reveals that they are composed of three distinct modular domains. The N‐terminal (N) and C‐terminal (C) domains areExpand
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Mitochondrial Carrier Homolog 2 Is a Target of tBID in Cells Signaled To Die by Tumor Necrosis Factor Alpha
ABSTRACT BID, a proapoptotic BCL-2 family member, plays an essential role in the tumor necrosis factor alpha (TNF-α)/Fas death receptor pathway in vivo. Activation of the TNF-R1 receptor results inExpand
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Automated construction and graphical presentation of protein blocks from unaligned sequences.
Protein blocks consist of multiply aligned sequence segments that correspond to the most highly conserved regions of protein families. Typically, a set of related proteins has more than one region inExpand
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