1994
DOI: 10.1006/jmbi.1994.1104
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Hidden Markov Models in Computational Biology

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Cited by 1,659 publications
(1,075 citation statements)
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References 30 publications
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“…Residues 918-1006 of endoglucanase C of C. fimi matched the HMM with a score of 34 bits. We would expect that a score of 17 bits would be a significant match in searching a database of the size of SWISS-PROT (Krogh et al, 1994;Eddy et al, 1995). This theoretical calculation is supported empirically by the 347 other domains, which were detected by the HMM with scores greater than 18.6, that have been described previously as IgSF members on the basis of characteristics of their sequences.…”
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confidence: 57%
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“…Residues 918-1006 of endoglucanase C of C. fimi matched the HMM with a score of 34 bits. We would expect that a score of 17 bits would be a significant match in searching a database of the size of SWISS-PROT (Krogh et al, 1994;Eddy et al, 1995). This theoretical calculation is supported empirically by the 347 other domains, which were detected by the HMM with scores greater than 18.6, that have been described previously as IgSF members on the basis of characteristics of their sequences.…”
mentioning
confidence: 57%
“…The evidence for this comes from a hidden Markov model (HMM) (Krogh et al, 1994;Eddy et al, 1995) of the IgSF protein fold, the BLASTP local sequence alignment tool (Altschul et al, 1990), key residue analysis (Chothia & Lesk, 1987;Harpaz & Chothia, 1994), and a prediction of their secondary structures by the PHD program (Rost & Sander, 1994) Nearly all the members of the immunoglobulin superfamily can be assigned to one of a number of different sets: V, C1, C2, and I (Williams & Barclay, 1988;Harpaz & Chothia, 1994). Members of one set are more similar to one another in sequence and structure than to members of the other sets.…”
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confidence: 99%
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“…Each grammar was used to parse sequences, computing a probability value. Sequence classification was performed based on z-score calculation (details in [78]). …”
Section: Comparative Methodsmentioning
confidence: 99%
“…In previous studies of this kind [for example, Gribskov et al (1987) and Krogh et al (1994)], the globin-recognition problem was treated as a sequence classification problem. However, such an approach simplifies the underlying biological problem since globin folding units, like most other protein structural domains, occasionally occur as multiple copies in the same polypeptide chain.…”
Section: The Globin -Recognition Problemmentioning
confidence: 99%