COMA

[…] remote homologues using the more sensitive hmm–hmm comparison. hhalign (https://toolkit.tuebingen.mpg.de/hhalign []) was used for testing possible homology between eboa and ebog (see §3.2) by direct comparison of multiple alignments of eboa and ebog sequences (the alignments were built with mafft using sequences collected from the ncbi nr protein database with psi-blast)., the relationship […]

[…] the genome between the origin of replication and orf v2 (position 14) and between orfs v3 and c3 (position 1841) in the genome with no effect on the integrity of orfs encoded by the virus. pairwise comparison of multiple alignments of individual orfs indicated that orfs encoded by grlav shared 99–100% and 98–100% identities at the nt and aa levels, respectively, with corresponding orfs of virus […]

[…] improvement of profile-based methods. further development of statistical framework is another promising area of improvement for both profile and hmm-based methods., here, we present coma (comparison of multiple alignments), a new profile-profile search and comparison method that has a number of novel features. however, the two features that distinguish coma from other profile-profile […]

[…] information from a pssm, hmm and amino-acid frequencies in the alignment to predict the secondary structure of syme (). the predicted structure was entirely congruent to that of the abrb fold (). comparison of multiple alignments of the syme family with classical members of the abrb superfamily indicated that they shared all the key hydrophobic residues, which constitute the core […]