[WashU] HMMER
User's Guide


| Dept. of Genetics | WashU | Medical School | Sequencing Center | CGM | IBC|
| Eddy lab | Internal (lab only) | HMMER | PFAM | tRNAscan-SE | Software | Publications |

... stuck.2.1
There has been some agitation to call all such models ``position specific scoring matrices'', PSSMs, but certain small nocturnal North American marsupials have a prior claim on the mnemonic.
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... scores.2.2
Surprisingly, this is still controversial. People have been saying ``there is no theory for setting gap scores'' for so long that many people believe it.
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... positions.2.3
This is not strictly true. There is a subtle difference between an HMM's state path (a first order Markov chain) and the sequence described by an HMM (generated from the state path by independent emissions of symbols at each state).
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... architecture2.4
The origin of the codename is obscure, involving both details of the state transition probability distributions in profile HMM architecture and an inordinate fondness for bad science fiction movies. Frighteningly, David Haussler understood the codename immediately.
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...$t(B\rightarrow D)$.4.1
OK, it's more complicated than it has to be. Sometimes you only discover your temporary insanity when you're trying to document it.
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Direct comments and questions to <eddy@genetics.wustl.edu>