Expressed sequence tags EST databases

When the Arabidopsis Expressed Sequence Tag (EST) Database was searched with the tomato fmit Psubunit protein sequence two related cDNAs were identified (Figure 11). cDNA 2 is near full length and has been completely sequenced, cDNA 1 has also been sequenced but currently lacks approximately 100 amino acids of coding region. The two Arabidopsis cDNAs are 81% identical at the protein level and have lower identity to the protein encoded by tomato gene 1, 64 and 63% for cDNA 1 and cDNA 2, respectively. However, both cDNAs encode... 

PMF is generally used to identify proteins that have been previously separated by 2-D GE so that additional information including the molecular weights and isoelectric points can be used to supplement PMF identification. PMF is not well suited for searching expressed sequence tag (EST) databases that contain incomplete gene coding information for particular ESTs and it is not adequate for the analysis of complex protein mixtures in solution. 

The second approach is the tandem mass spectrometric method (Wilm et ah, 1996 Link et ah, 1999 Yates, 2000). This method relies on fragmentation of individual peptides in the tryptic peptide mixture to gain sequence information. Its main advantage is that sequence information derived from several peptides is much more specific for the identification of a protein than a list of peptide masses. The sequence data can be used to search not only protein sequence databases but also nucleotide databases such as expressed sequence tag (EST) databases and, more recently, even... 

The advent of rapid DNA cloiung and sequencing techniques, and the pubhc availability of nucleotide sequence information from the tikes of ttie tiuman genome sequencing project, various expressed sequence tag (EST) databases, and various... 

Figure 15.3 Producing expressed sequence tag (EST) databases by random DNA sequencing of cDNA libraries...

As of 2003, a novel class of starch synthase amino acid sequences designated as SSIV was noted in expressed sequence tag (EST) databases from several species including Arabidopsis, Chlamydomonas, wheat, and cow pea. ... 

In the past six years, a large number of new chemokines and chemokine receptors have been discovered and characterized. This is mainly attributed to the rapid progress in the area of bioinformatics and expressed sequence tag (EST) databases. It is now clear that chemokine function is not just restricted to cell attraction. Chemokines are also important in mediating the development and functional aspects of leukocytes. Recent discoveries provide convincing and compelling evidences supporting the roles of these messengers and their receptors in the resolution of viral infections and virus survival. 

The identification of proteins with MS/MS is a powerful technique specially for the identification of protein mixtures [160]. There is also the possibility to search in expressed sequence tags (EST) databases [161]. However, it is also important to note that many more modifications are possible when fragmenting the peptides, which result in exponential combinatorial possibilities of search. 

---