Sequence tagging

EST Expressed sequence tag. An EST is a partial sequence (typically less than 40C bases) selected from cDNA and used to identify genes expressed in a particuh tissue... 

ITS Sequence tagged site. A short DNA sequence that occurs just once in the human genome and whose location and base sequence are known... 

G. J. Opiteck, J. W. Jorgenson, M. A. Moseley III and R. J. Anderegg, Two-dimensional mia ocolumn HPLC coupled to a single-quadrupole mass spectrometer for the elucidation of sequence tags and peptide mapping , 7. Microcolumn Sep. 10 365-375 (1998). 

Expressed Sequence Tag. A short DNA sequence usually representing the most terminal regions of a cDNA clone. 

This process, sometimes known as sequence tagging, may be a more convenient method of obtaining sequence information but it has to be said that it is unlikely to allow as many residues to be determined as when using the classical Edman approach. 

Sequence tagging The use of MS-MS to investigate the amino acid sequence of a peptide. 

Abbreviations STS, sequence tagged site RFLP, restriction fragment iinked poiymorphism SNP, singie nucieotide poiymorphism YAC, yeast artificiai chromosome BAC, bacteriai artificiai chromosome PCR, poiymerase chain reaction. 

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... 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Mann, M. (1996). A shortcut to interesting human genes peptide sequence tags, expressed-sequence tags and computers. Trends Biochem. Sci. 21, 494-495. 

The PepSeq program of Micromass s ProteinLynx software package was used for de novo analysis of the sequence (MS/MS) data. MS-Pattern of ProteinProspectror55 used the sequence tag determined from PepSeq to search the nonredundant database of the National Center for Biotechnology Information (NCBI) for protein identification. 

Mann, M. Wilm, M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 1994, 66,4390-4399. 

Mortz, E. O Connor, P. B. Roepstorff, P. Kelleher,N. L. Wood,T. D. McLafferty, F. W. Mann, M. Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases. Proc Nat. Acad. Sci. USA 1996, 93, 8264-8267. 

TES-32 is the most abundant single protein product secreted by the parasite. It is also heavily labelled by surface iodination of live larvae (Maizels et al., 1984, 1987), and is known by monoclonal antibody reactivity to be expressed in the cuticular matrix of the larval parasite (Page et al, 1992a). TES-32 was cloned by matching peptide sequence derived from gel-purified protein to an expressed sequence tag (EST) dataset of randomly selected clones from a larval cDNA library (Loukas et al., 1999). Because of the high level of expression of TES-32 mRNA, clones encoding this protein were repeatedly sequenced and deposited in the dataset (Tetteh et al., 1999). Full sequence determination showed a major domain with similarity to mammalian C-type (calcium-dependent) lectins (C-TLs), together with shorter N-terminal tracts rich in cysteine and threonine residues. Native TES-32 was then shown to bind to immobilized monosaccharides in a calcium-dependent manner (Loukas et al., 1999). 

Tetteh, K.K.A., Loukas, A., Tripp, C. and Maizels, R.M. (1999) Identification of abundantly-expressed novel and conserved genes from infective stage larvae of Toxocara canis by an expressed sequence tag strategy. Infection and Immunity 67, 4771-4779. 

Welage, L. Barnett, C. P. Landowski, D. Foster, D. Fleisher, K.-D. Lee et al. Comparison of Human Duodenum and Caco-2 Gene Expression Profiles for 12,000 Gene Sequences Tags and Correlation with Permeability of 26 Drugs., Pharm. Res. 2002, 29, 1400-1416... 

Sun, D., et al. Comparison of human duodenum and Caco-2 gene expression profiles for 12,000 gene sequences tags and correlation with permeability of 26 drugs. Pharm. Res. 2002, 19, 1400-1416. 

Expressed Sequence Tags (ESTs) and Computational Biology ... 

Xiao H, Merril, CR, Wu A, Olde B, Moreno R, Kerlavage AR, McCombie WR, Venter JC. Complementary DNA sequencing Expressed Sequence Tags and the Human Genome Project. 

Adams MD et al. 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nature Genet 1993 4 256-267. 

Ewing B et al. Analysis of expressed sequence tags indicates 35,000 human genes. Nature Genet 2000 25 232-234. 

C, Charmley P, Kaiser R, Hood L. Identification of clusters of biallelic polymorphic sequence-tagged sites (pSTSs) that generate highly informative and... 

Ulrich CM, Bigler J, Velicer CM et al. Searching expressed sequence tag databases discovery and confirmation of a common polymorphism in the thymidylate synthase gene. Cancer Epidemiol Biomarkers Prev 2000 9 1381-1385. 

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