Abstract
The Blocks server allows access to multiply aligned ungapped sequence segments corresponding to the most highly conserved regions of proteins, and aids detection and verification of protein sequence homologies using both DNA and protein as a starting material.
Highlights
The Blocks server allows access to multiply aligned ungapped sequence segments corresponding to the most highly conserved regions of proteins, and aids detection and verification of protein sequence homologies using both DNA and protein as a starting material
The output from a Block Search query is represented in a classic sequence-alignment format. It would very convenient if the same information were represented graphically so that the location of the identified block could be immediately placed on the query protein
There are many websites aimed at recognizing local regions of similarity between the entire pool of protein sequences held on a given database, and the Blocks server will automatically screen through three major databases Pfam, ProDom and Domo, all of which are linked from the SearchBlocks page
Summary
The Block Searcher compares a sequence of a newly identified DNA or protein against the current database of protein blocks. The advantage of searching a database of blocks is that information from multiply aligned sequences is present in a concentrated unbiased form, reducing background 'noise' and increasing sensitivity to distant relationships Such a tool can give an indication of the evolutionary origins of a protein, and an indication of its function, without the query protein containing wellcharacterized functional motifs per se. Another very useful feature of the Blocks server is the 'codehop' (consensus-degenerate hybrid oligonucleotide primers) function (see related report - Genome Biology 1(1):reports[240]) This program allows retrieval of a protein block direct from the database (for example, using the keyword 'homeobox' from the GetBlocks function) followed by a user-driven automated process for the design of degenerate oligonucleotide primers. These primers are useful for both degenerate reverse-transcription PCR, and for other methods such as targeted differential display analysis
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Published Version
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