hmm-file

TXT

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

🔙 To the main page of anvi’o programs and artifacts.

Provided by

There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

Required or used by

anvi-script-gen-defense-finder-models-to-hmm-directory anvi-script-hmm-to-hmm-directory

Description

A flat text HMM that literally desribes the properties of the model and lists transition probabilities.

Such files are typically generated by the program hmmbuild (which is a part of the HMMER package and installed in every anvi’o environment) from FASTA files of gene amino acid sequence alignments. A properly formatted hmm-file will look more or less like this:

HMMER3/f [3.3 | Nov 2019]
NAME  NusB
ACC   PF01029.22
DESC  NusB family
LENG  133
ALPH  amino
RF    no
MM    no
CONS  yes
CS    no
MAP   yes
DATE  Sat Apr 29 10:48:13 2023
NSEQ  63
EFFN  5.564026
CKSUM 2756372009
GA    23.1 23.1;
TC    23.1 23.1;
NC    23 23;
BM    hmmbuild HMM.ann SEED.ann
SM    hmmsearch --cpu 4 -E 1000 -Z 75585367 HMM pfamseq
STATS LOCAL MSV       -9.6745  0.71150
STATS LOCAL VITERBI  -10.4604  0.71150
STATS LOCAL FORWARD   -4.0120  0.71150
HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y
            m->m     m->i     m->d     i->m     i->i     d->m     d->d
  COMPO   2.38570  4.55521  2.97888  2.58191  3.42062  3.17155  3.83378  2.76365  2.65171  2.28201  3.70599  2.97075  3.61609  3.06259  2.79156  2.76589  2.94655  2.57771  4.76753  3.56330
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
          0.11400  5.43890  2.26918  0.61958  0.77255  0.00000        *
      1   2.84469  5.43592  3.17480  2.76604  4.73974  3.82086  2.84921  3.79498  2.55661  2.95708  2.50274  2.99752  3.37273  2.77536  2.08861  2.33124  2.32432  3.46807  5.89412  4.50954      1 r - - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
          0.00721  5.33210  6.05445  0.61958  0.77255  0.37903  1.15367
      2   2.56574  5.58242  2.92442  2.33486  4.92712  3.57653  4.03367  3.34225  2.02562  3.26845  4.62318  2.23324  3.17894  2.58384  2.54233  2.40058  2.79834  3.38823  6.01533  4.60460      2 k - - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
          0.00658  5.42266  6.14500  0.61958  0.77255  0.44543  1.02318
      3   1.37170  5.20503  3.33911  2.84075  4.41845  3.95135  4.16211  3.07174  2.99075  3.11149  3.93574  3.22883  3.05438  3.33495  2.96504  2.22852  2.50816  2.79614  5.72578  4.41195      3 a - - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
          0.00647  5.43890  6.16124  0.61958  0.77255  0.48576  0.95510
     (...)

Edit this file to update this information.

Copyleft, The anvi'o Project