Protein Sequence Analysis Group

Bioinformatics Institute
  Supplementary materials to:
  The Janus-faced E-values of HMMER2: Extreme value distribution or logistic function

Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber

Full reference
Journal of Bioinformatics and Computational Biology, v9, n1, doi: 10.1142/S0219720011005264

Supplementary file 1
Hmmpfam output of the Pfam domain PF00311.9 (Phosphoenolpyruvate carboxylase) when searched against the non-redundant database. We used the command "hmmsearch -Z 10340" to annotate sequences with just this particular domain and to have E-values that equal to those searched with hmmpfam. The results contain true hits with extremely low E-values as well as good hits with large E-values. The E-value space in between the extremes is undersampled.

Filename : Janus-Suppl-File-1.pdf (4,477kb) download

Supplementary file 2
Source code of 'Mathsupport.c' in HMMER2 package with additional commentary lines.

Filename : Janus-Suppl-File-2.pdf (27kb) download

Supplementary file 3
Detail information associated to the 185 and 1748 domain models detected by global-mode hmmpfam and hmmsearch respectively.

Filename : Janus-Suppl-File-3.xls (660kb) download

Supplementary file 4
The concatenated HMMER2 outputs of the nine false-positive hits detected by global-mode hmmpfam as listed in Table 1 and illustrated in Figure 4.

Filename : Janus-Suppl-File-4.txt (46kb) download

Supplementary file 5
The concatenated HMMER2 outputs of the seven false-positive hits detected by global-mode hmmsearch as listed in Table 2 and illustrated in Figure 5.

Filename : Janus-Suppl-File-5.txt (48kb) download

Supplementary file 6
The archive (in WinRAR format) of the 24 outlier Pfam domains with small and large negative listed in Table 3. Note that the WinRAR program is a file archive manager that can be downloaded at

Filename : Janus-Suppl-File-6.rar (1,833kb) download

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