AnaGram: protein function assignment.

SUMMARY: AnaGram is a web service for protein function assignment based on identity detection of small significant fragments (protomotifs) that can act as modular pieces in peptide construction. The system is able to assign function by finding correlations between protomotifs and functional annotations contained in SWISS-PROT and Medline databases. In addition, function ontologies are used for hierarchical organization of the predicted functions. Extensive tests have been carried out to evaluate the accuracy and performance of the system. AVAILABILITY: http://jaguar.genetica.uma.es/anagram.htm

Poly(A) site choice during mRNA 3'-end formation in the Schizosaccharomyces pombe wos2 gene.

In the fission yeast Schizosaccharomyces pombe, the wos2 gene encodes p23, a highly conserved protein which functions as a co-chaperone for the heat shock protein Hsp90. This p23 protein binds to Hsp90, but its activities and regulatory mechanisms are still unclear. Northern analysis has shown that the wos2 gene produces three transcripts of about 1.1, 0.9 and 0.8 kb, which are expressed differentially depending on the growth temperature. The largest and the smallest transcripts were most abundant at 25 degrees C, whereas the 0.9-kb transcript predominated at 37 degrees C. A time-course analysis indicated that this 0.9-kb species rapidly increased in abundance after a shift from 25 degrees C to 37 degrees C, reaching a maximum after 15 min. A shift back to 25 degrees C resulted in a decline in the amount of this transcript, albeit at a slower rate. Expression analysis of wos2:ura4 and nmt1:wos2 constructs showed that the 3' untranslated region of wos2 alone directs the formation of these multiple, discrete wos2 mRNAs. Sequence analysis of cDNAs derived from these mRNAs showed that the use of different polyadenylation sites results in the production of the three differently sized wos2 transcripts. In the case of the 0.9- and 0.8-kb mRNA species, these sites lie in a predicted hairpin loop in the mRNA, suggesting that polyadenylation signals in wos2 transcripts may be mediated by RNA secondary structure. The possibility that differential thermal stability of these hairpin structures could influence polyadenylation site choice during formation of the 3'-ends of the mRNAs is discussed.

A computational strategy for protein function assignment which addresses the multidomain problem.

A method for assigning functions to unknown sequences based on finding correlations between short signals and functional annotations in a protein database is presented. This approach is based on keyword (KW) and feature (FT) information stored in the SWISS-PROT database. The former refers to particular protein characteristics and the latter locates these characteristics at a specific sequence position. In this way, a certain keyword is only assigned to a sequence if sequence similarity is found in the position described by the FT field. Exhaustive tests performed over sequences with homologues (cluster set) and without homologues (singleton set) in the database show that assigning functions is much 'cleaner' when information about domains (FT field) is used, than when only the keywords are used.

Search for ancient patterns in protein sequences.

Proteins of related functions are often similar in sequence, reflecting a common phylogenetic origin. Proteins with no known homology are probably diversified proteins, too distantly related to known sequences in databases to retain significant similarity. All proteins, however, probably share common ancestries if one moves far enough back in evolution; therefore, given the huge accumulation of protein sequences in current databases, it could be expected that some proteins with no obvious sequence resemblance to any other share some residues that could represent footprints of ancient common ancestries. To identify such putative footprints, we have searched for short stretches of amino acids present in a given protein sequence that are also found in a significant number of nonrelated proteins in the database. The significantly high frequency of occurrence of these "patterns" in the database would support a common evolutionary source, and a diversity of non-related proteins that contain the pattern would express their ancient origin. Using this strategy, significant patterns were found in actual exons, but not in randomized amino acid sequences, nor in "translated" sequences of noncoding DNA, suggesting that this strategy actually leads to the identification of patterns with a biological significance. These significant patterns are not randomly positioned along the sequences analyzed, but they tend to accumulate within specific regions, producing a profile of discrete "domains." In some well-known proteins analyzed in this study, some of these domains are coincident with known motifs. Thus, the procedure described in this paper could be useful for identifying ancient patterns and domains in protein sequences, some of which could also have a functional or structural significance.

Chromosome complement, C-banding, Ag-NOR and replication banding in the zebrafish Danio rerio.

The chromosome complement of Danio rerio was investigated by Giemsa staining and C-banding, Ag-NORs and replication banding. The diploid number of this species is 2n = 50 and the arm number (NF) = 100. Constitutive heterochromatin was located at the centromeric position of all chromosome pairs. Nucleolus organizer regions appeared in the terminal position of the long arms of chromosomes 1, 2 and 8. Replication banding pattern allowed the identification of each chromosome pair.