Using the Blocks Database to Recognize Functional Domains
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- Abstract
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- Literature Cited
Abstract
Blocks are ungapped multiple alignments of related protein sequence segments that correspond to the most conserved regions of the proteins. The Blocks Database is a collection of blocks representing known protein families that can be used to compare a protein or DNA sequence with documented families of proteins. Protocols in this unit describe the analysis of proteins and families using Blocks?based tools, including searching, exploring relationships with trees, making new blocks, and designing PCR primers from blocks for isolating homologous sequences.
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- Basic Protocol 1: Exploring Protein Families Using the Blocks Database
- Support Protocol 1: Search Blocks Versus Other Databases
- Basic Protocol 2: Analyzing Protein Sequences with the Block Searcher
- Basic Protocol 3: Analyzing DNA Sequences with the Block Searcher
- Basic Protocol 4: Viewing Trees Based on Blocks
- Basic Protocol 5: Using Block Maker
- Basic Protocol 6: Designing Primers from Blocks
- Guidelines for Understanding Results
- Commentary
- Figures
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Basic Protocol 1: Exploring Protein Families Using the Blocks Database
Necessary Resources
Support Protocol 1: Search Blocks Versus Other Databases
Necessary Resources
Basic Protocol 2: Analyzing Protein Sequences with the Block Searcher
Necessary Resources
Basic Protocol 3: Analyzing DNA Sequences with the Block Searcher
Necessary Resources
Basic Protocol 4: Viewing Trees Based on Blocks
Necessary Resources
Basic Protocol 5: Using Block Maker
Necessary Resources
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Figure 2.2.1 The Blocks Web site home page (http://blocks.fhcrc.org). View Image -
Figure 2.2.2 Top of the Blocks Database entry page for the C‐5 cytosine‐specific DNA methylase family. The blocks accession number is IPB001525 and the sequences used to make the blocks were taken from InterPro entry IPR001525. View Image -
Figure 2.2.3 One page of the second block representing the C‐5 cytosine‐specific DNA methylase family, IPB001525B, showing the block header lines and some of the 158 sequence segments included in the block. View Image -
Figure 2.2.4 Sequence logos for the IPB001525 blocks, showing the multiple alignments graphically. View Image -
Figure 2.2.5 3D Blocks output for 6MHT showing the IPB001525 blocks on the structure. View Image -
Figure 2.2.6 Part of the MAST output generated by selecting the MAST Search link in Figure . The query in this search was constructed from six position‐specific scoring matrices computed from the six IPB001525 blocks, and the database was Drosophila protein sequences. GenBank entry AAF53163.1 is the top hit. View Image -
Figure 2.2.7 The upper part of the Block Searcher input form. View Image -
Figure 2.2.8 The Block Searcher result from searching GenBank entry AAF53163.1 against the Blocks Database, showing five of the six IPB001525 blocks in the top hit. View Image -
Figure 2.2.9 Segment of GenBank AE003635.1 that includes the AAF53163.1 coding region. The DNA sequence is used with Block Searcher to overcome an error in AAF53163.1. View Image -
Figure 2.2.10 The Block Searcher result from searching a segment of GenBank entry AE003635.1 against the Blocks Database, showing all six of the IPB001525 blocks in the top hit. The query most closely resembles PMT1_SCHPO in blocks A, C, E, and F. View Image -
Figure 2.2.11 Corrected version of protein sequence AAF53163.1. View Image -
Figure 2.2.12 The first page of a phylogenetic tree made from the block regions of the 158 sequences included in IPB001525 as displayed by the ProWeb TreeViewer. View Image -
Figure 2.2.13 The subclade of the IPB001525 tree that includes PMT1_SCHPO as displayed by the ProWeb TreeViewer showing options for subclade analysis, including a link to Block Maker. View Image -
Figure 2.2.14 The Block Maker input form obtained by clicking the Block Maker link in Figure with the full‐length sequences for the subclade inserted. View Image -
Figure 2.2.15 The Block Maker result from the subclade selected in Figure plus the corrected Dnmt2 sequence (Fig. ) using the MOTIF motif finder. View Image -
Figure 2.2.16 The Block Maker result from the subclade selected in Figure plus the corrected Dnmt2 sequence (Fig. ) using the Gibbs motif finder. View Image -
Figure 2.2.17 The CODEHOP input form obtained by clicking the CODEHOP link in Figure with the Block Maker Gibbs blocks inserted. View Image -
Figure 2.2.18 Part of the CODEHOP result showing suggested PCR primers with maximum degeneracy set to 32. View Image
Videos
Literature Cited
| Literature Cited | |
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| Pietrokovski, S., Henikoff, J.G., and Henikoff, S. 1998. Exploring protein homology with the Blocks server. Trends Genet. 14:162‐163. | |
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| Rose, T.M., Schultz, E.R., Henikoff, J.G., Pietrokovski, S., McCallum, C.M., and Henikoff, S. 1998. Consensus‐degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 26:1628‐1635. | |
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| Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position‐specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673‐4680. | |
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| Key References | |
| Henikoff and Henikoff, 1991. See above. | |
| Introduces the Blocks Database, how it is constructed using PROTOMAT and how it is searched using Block Searcher. | |
| Pietrokovski, 1996. See above. | |
| Introduces LAMA for searching blocks versus a database of blocks as an example of searching multiple alignments against one another for sensitive detection of motifs. | |
| Rose et al., 1998. See above. | |
| Describes the CODEHOP strategy for detecting distant homologs using PCR and the Web‐based implementation for designing optimal CODEHOP primers. | |
| Internet Resources | |
| http://blocks.fhcrc.org | |
| This is the Blocks Web page. | |
| http://www.proweb.org | |
| This is the ProWeb Web page. |
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