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Literature DB >> 9016540

Recent enhancements to the Blocks Database servers.

J G Henikoff¹, S Pietrokovski, S Henikoff.

Abstract

The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail (blocks@blocks.fhcrc.org) and World Wide Web (http://blocks.fhcrc.org/ ) servers to classify protein and nucleotide sequences. Recent enhancements to the servers include: (i) improved calculation of position-specific scoring matrices from blocks; (ii) availability of the Prints protein fingerprint database for searching in Blocks format; (iii) a representative sequence biased towards the Blocks of a protein family; (iv) a tree constructed from the Blocks of a protein family; (v) links to related World Wide Web pages for a family; and (vi) the new Local Alignment of Multiple Alignments (LAMA) method to search a block against a database of blocks.

Mesh：

Substances：
Proteins

Year: 1997 PMID： 9016540 PMCID： PMC146414 DOI： 10.1093/nar/25.1.222

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

26 in total

1. Amino acid substitution matrices from protein blocks.

Authors: S Henikoff; J G Henikoff
Journal: Proc Natl Acad Sci U S A Date: 1992-11-15 Impact factor: 11.205

2. Automated construction and graphical presentation of protein blocks from unaligned sequences.

Authors: S Henikoff; J G Henikoff; W J Alford; S Pietrokovski
Journal: Gene Date: 1995-10-03 Impact factor: 3.688

3. Blocks database and its applications.

Authors: J G Henikoff; S Henikoff
Journal: Methods Enzymol Date: 1996 Impact factor: 1.600

4. Using substitution probabilities to improve position-specific scoring matrices.

Authors: J G Henikoff; S Henikoff
Journal: Comput Appl Biosci Date: 1996-04

5. Using Dirichlet mixture priors to derive hidden Markov models for protein families.

Authors: M Brown; R Hughey; A Krogh; I S Mian; K Sjölander; D Haussler
Journal: Proc Int Conf Intell Syst Mol Biol Date: 1993

6. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.

Authors: C E Lawrence; S F Altschul; M S Boguski; J S Liu; A F Neuwald; J C Wootton
Journal: Science Date: 1993-10-08 Impact factor: 47.728

7. Position-based sequence weights.

Authors: S Henikoff; J G Henikoff
Journal: J Mol Biol Date: 1994-11-04 Impact factor: 5.469

8. PRINTS--a protein motif fingerprint database.

Authors: T K Attwood; M E Beck
Journal: Protein Eng Date: 1994-07

9. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.

Authors: R L Tatusov; S F Altschul; E V Koonin
Journal: Proc Natl Acad Sci U S A Date: 1994-12-06 Impact factor: 11.205

10. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors: J D Thompson; D G Higgins; T J Gibson
Journal: Nucleic Acids Res Date: 1994-11-11 Impact factor: 16.971

15 in total

Review 1. The Mrp system: a giant among monovalent cation/proton antiporters?

Authors: Talia H Swartz; Sayuri Ikewada; Osamu Ishikawa; Masahiro Ito; Terry Ann Krulwich
Journal: Extremophiles Date: 2005-06-25 Impact factor: 2.395

2. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis.

Authors: S Henikoff; L Comai
Journal: Genetics Date: 1998-05 Impact factor: 4.562

3. Superior performance in protein homology detection with the Blocks Database servers.

Authors: S Henikoff; S Pietrokovski; J G Henikoff
Journal: Nucleic Acids Res Date: 1998-01-01 Impact factor: 16.971

4. The PRINTS protein fingerprint database in its fifth year.

Authors: T K Attwood; M E Beck; D R Flower; P Scordis; J N Selley
Journal: Nucleic Acids Res Date: 1998-01-01 Impact factor: 16.971

5. The rat gene homologous to the human gene 9-27 is involved in the development of the mammary gland.

Authors: I Zucchi; C Montagna; L Susani; P Vezzoni; R Dulbecco
Journal: Proc Natl Acad Sci U S A Date: 1998-02-03 Impact factor: 11.205

6. SMART, a simple modular architecture research tool: identification of signaling domains.

Authors: J Schultz; F Milpetz; P Bork; C P Ponting
Journal: Proc Natl Acad Sci U S A Date: 1998-05-26 Impact factor: 11.205

7. Highly specific protein sequence motifs for genome analysis.

Authors: C G Nevill-Manning; T D Wu; D L Brutlag
Journal: Proc Natl Acad Sci U S A Date: 1998-05-26 Impact factor: 11.205

8. Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2.

Authors: R Tavares; S Aubourg; A Lecharny; M Kreis
Journal: Plant Mol Biol Date: 2000-03 Impact factor: 4.076

9. Genetic dissection of dome formation in a mammary cell line: identification of two genes with opposing action.

Authors: I Zucchi; C Montagna; L Susani; R Montesano; M Affer; S Zanotti; E Redolfi; P Vezzoni; R Dulbecco
Journal: Proc Natl Acad Sci U S A Date: 1999-11-23 Impact factor: 11.205

10. The arabinose kinase, ARA1, gene of Arabidopsis is a novel member of the galactose kinase gene family.

Authors: S Sherson; I Gy; J Medd; R Schmidt; C Dean; M Kreis; A Lecharny; C Cobbett
Journal: Plant Mol Biol Date: 1999-03 Impact factor: 4.076