Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this problem. PHMM packages such as HMMER and SAM perform particularly well at recognising distant homologies, while presenting a relatively small computational cost. This led several researchers to study pHMM performance, measured from their accuracy and sensitivity. Results do show improvements depending on training and configuration parameters. However, and to the best of our knowledge, there has been no research so far on whether structural alignments could impact pHMM performance, even though structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using of structural alignment in pHMM performance.
http://wiki.biowebdb.org/images/PerlLib.tar.gz (Perl Library required to run our perl scripts)
http://wiki.biowebdb.org/images/Scripts.tar.gz (All perl scripts used in our study)
http://wiki.biowebdb.org/images/HMMER_mammoth_results.tar.gz (HMMER mammoth results)
http://wiki.biowebdb.org/images/HMMER_mammoth_models.tar.gz (HMMER mammoth models created from mammoth alignment)
http://wiki.biowebdb.org/images/HMMER_3dcoffee_results.tar.gz (HMMER 3dcoffee results)
http://wiki.biowebdb.org/images/HMMER_3dcoffee_models.tar.gz (HMMER 3dcoffee models created from 3dcoffee alignment)
http://wiki.biowebdb.org/images/HMMER_tcoffee_results.tar.gz (HMMER tcoffee results)
http://wiki.biowebdb.org/images/HMMER_tcoffee_models.tar.gz (HMMER tcoffee models created from tcoffee alignment)
http://wiki.biowebdb.org/images/HMMER_clustalw_results.tar.gz (HMMER clustalw results)
http://wiki.biowebdb.org/images/HMMER_clustalw_models.tar.gz (HMMER clustalw models created from clustalw alignment)
http://wiki.biowebdb.org/images/SAM_mammoth_results.tar.gz (SAM mammoth results)
http://wiki.biowebdb.org/images/SAM_mammoth_models_2.tar.gz (SAM mammoth models (part 2) created from mammoth alignment)
http://wiki.biowebdb.org/images/SAM_mammoth_models_1.tar.gz (SAM mammoth models (part 1) created from mammoth alignment)
http://wiki.biowebdb.org/images/SAM_3dcoffee_results.tar.gz (SAM 3dcoffee results)
http://wiki.biowebdb.org/images/SAM_3dcoffee_models_2.tar.gz (SAM 3dcoffee models (part 2) created from 3dcoffee alignment)
http://wiki.biowebdb.org/images/SAM_3dcoffee_models_1.tar.gz (SAM 3dcoffee models (part 1) created from 3dcoffee alignment)
http://wiki.biowebdb.org/images/SAM_tcoffee_results.tar.gz (SAM tcoffee results)
http://wiki.biowebdb.org/images/SAM_tcoffee_models_2.tar.gz (SAM tcoffee models (part 2) created from tcoffee alignment)
http://wiki.biowebdb.org/images/SAM_tcoffee_models_1.tar.gz (SAM tcoffee models (part 1) created from tcoffee alignment)
http://wiki.biowebdb.org/images/SAM_clustalw_results.tar.gz (SAM clustalw results)
http://wiki.biowebdb.org/images/SAM_clustalw_models_2.tar.gz (SAM clustalw models (part 2) created from clustalw alignment)
http://wiki.biowebdb.org/images/SAM_clustalw_models_1.tar.gz (SAM clustalw models created from clustalw alignment)
http://wiki.biowebdb.org/images/Family_list.table.tar.gz (Family list)
http://wiki.biowebdb.org/images/Pdbs_4.tar.gz (Pdb files (part 4) dataset for structural alignment)
http://wiki.biowebdb.org/images/Pdbs_3.tar.gz (Pdb files (part 3) dataset for structural alignment)
http://wiki.biowebdb.org/images/Pdbs_2.tar.gz (Pdb files (part 2) dataset for structural alignment)
http://wiki.biowebdb.org/images/Pdbs_1.tar.gz (Pdb files (part 1) dataset for structural alignment)
http://wiki.biowebdb.org/images/Sequences.tar.gz (Sequences for alignment)
http://wiki.biowebdb.org/images/Mammoth_alignment_G.tar.gz (Mammoth alignment G super-families dataset)
http://wiki.biowebdb.org/images/Mammoth_alignment_D.tar.gz (Mammoth alignment D super-families dataset)
http://wiki.biowebdb.org/images/Mammoth_alignment_C.tar.gz (Mammoth alignment C super-families dataset)
http://wiki.biowebdb.org/images/Mammoth_alignment_B.2.tar.gz (Mammoth alignment B (part 2) super-families dataset)
http://wiki.biowebdb.org/images/Mammoth_alignment_B.1.tar.gz (Mammoth alignment B (part 1) super-families dataset)
http://wiki.biowebdb.org/images/Mammoth_alignment_A.tar.gz (Mammoth alignment A super-families dataset)
http://wiki.biowebdb.org/images/Mammoth_a.tar.gz (Mammoth alignment A super-families dataset)
http://wiki.biowebdb.org/images/3dcoffee_alignment.tar.gz (3dcoffee alignment dataset)
http://wiki.biowebdb.org/images/Clustalw_alignment.tar.gz (Clustalw alignment dataset)
http://wiki.biowebdb.org/images/Tcoffee_alignment.tar.gz (Tcoffee alignmnet dataset)
http://wiki.biowebdb.org/images/Astral_scop_40.database.tar.gz (Astral Scop Database)