The Pfam protein families database
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Cites background from "The Pfam protein families database"
...There are already widely available collections of HMMs from many sources such as Pfam...
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References
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"The Pfam protein families database" refers methods in this paper
...Generating new families using jackhmmer iterative searches The HMMER3 package (http://hmmer.janelia.org/) includes the jackhmmer (6) program for running iterative, profile HMM-based searches against a sequence database (PSI-BLAST-like) starting with a single sequence....
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...The HMMER3 project has four main aims: (i) to adopt log-odds likelihood scores summed over alignment uncertainty (Forward scores) in place of optimal alignment (Viterbi) scores; (ii) to report posterior probabilities of alignment confidence; (iii) to be able to accurately and quickly calculate expectation values (E-values) for Forward scores (a previously unsolved problem); and (iv) to accelerate previous profile HMM performance by two orders of magnitude and achieve an overall speed competitive with BLAST (2)....
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...Briefly, the ADDA algorithm takes a set of nonredundant sequences (11,12) and aligns them all-versus-all using BLAST (2)....
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"The Pfam protein families database" refers methods in this paper
...The static images are generated using Molscript ( 12 ) and rendered using Raster3D (13)....
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"The Pfam protein families database" refers methods in this paper
...These predictions are pre-computed over the sequence database by the following third party programs: TMHMM ( 10 ) (transmembrane regions), SignalP (11) (signal peptide regions), ncoils (12) (coiled-coil regions) and SEG (9) (low complexity regions)....
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