Increased coverage of protein families with the Blocks Database servers

By Jorja G. Henikoff, E. Greene, Shmuel Pietrokovski, Steven Henikoff. Nucleic Acids Res., 2000

347 citations recorded by the source corpus.

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Citations in the corpus

NetAffx: Affymetrix probesets and annotations (2003, methodology): “Protein sequences are annotated using public databases including Pfam (6) and BLOCKS (7), and in-house libraries of hidden Markov models (HMMs) trained for recognition of SCOP, EC and GPCR protein families.”
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. (2003, methodology): “The protocol of the profile–profile comparison (LAMA) with no gaps permitted was developed by Pietrokovski(13) for the comparisons of pairs of blocks from the BLOCKS database.(14,15) This protocol was further used in the CYRCA method(16) to identify multiple consistently aligned blocks within two co”
The InterPro database, an integrated documentation resource for protein families, domains and functional sites (2001, positive): “In addition, the Blocks database is now using InterPro to replace their old Blocks from PROSITE (J.Henikoff, personal communication).”
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment (2015, background): “Very large datasets such as BLOCKS [68] are still insufficient to accurately determine the frequency of many amino acid quadruplets [67].”
Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs (2001, methodology): “1997), a Hidden Markov model software which uses statistical descriptions of a sequence family’s consensus; and BLIMPS (Wallace and Henikoff 1992) for similarity searches against the BLOCKS (Henikoff et al. 2000) database.”
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins (2003, background): “There are now several globular protein domain databases accessible on the web, including Pfam (3), SMART (4), PROSITE (5), INTERPRO (6), PRODOM (7) and BLOCKS (8).”
InterPro-an integrated documentation resource for protein families, domains and functional sites (2000, background): “…include: PROSITE, regular expressions and proﬁles (Hofmann et al. , 1999); Pfam, hidden Markov models (HMMs) (Bateman et al. , 2000); PRINTS, ﬁngerprints (groups of aligned, un-weighted motifs) (Attwood et al. , 2000); and Blocks, aligned, weighted motifs or blocks (Henikoff et al. , 2000).”
PRINTS and its automatic supplement, prePRINTS (2003, methodology): “Several other incarnations of PRINTS are also available for searching, including a Blocks-format version at the Fred Hutchinson Cancer Research Center (9), the EMOTIF database Figure 2.”