Assignment 2: dbSTS

Deadline: Dec06, 2002

Database tour : http://www.ncbi.nlm.nih.gov/dbSTS,

Try to summarize and post what you can learn from this database in your own homepage.

Guidelines :

- What’s the database all about?

- Are there any tools in the database?, Please, provide some definition of those tools and give one example from those tools

(steps by step)

- What’s the strength and weakness of this database when compare with other database?

Database of sequence tagged sites (dbSTS) is an NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites.

In summary, this webpage provide informations for..

Definitions of STS and dbSTS as above.

How to submit to dbSTS include with details about data.

Tools for STS also provided.

About STS

Sequenced Tagged Sites (STSs) are short (about 200-500 bp) sequences that are operationally unique in a genome (i.e., can be specifically detected by PCR in the presence of all other genomic sequences), and that define a specific position on the physical map. STSs can therefore be used to generate mapping reagents which map to single positions within the genome.

STSs are usually submitted to GenBank and dbSTS as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format.

How to submission to dbSTS

This topic provides many details about submission; file types, agreement of processing of data files, mailing to data files to dbSTS, validation and updating data.

Tools provided in this webpage.

BLAST: Basic Local Alignment Search Tool is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. The BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity to distant sequence relationships. The scores assigned in a BLAST search have a well-defined statistical interpretation, making real matches easier to distinguish from random background hits. BLAST uses a heuristic algorithm which seeks local as opposed to global alignments and is therefore able to detect relationships among sequences which share only isolated regions of similarity (Altschul et al., 1990). For a better understanding of BLAST you can refer to the BLAST Course which explains the basics of the BLAST algorithm. There is also a description of BLAST services located here. Also for details on BLAST and theory of similarity search, see the references section.

UniSTS: NCBI resource that reports information about markers, or Sequence Tagged Sites (STS).

For each marker, UniSTS displays the primer sequences, product size, and mapping information, as well as cross references to LocusLink, dbSNP, RHdb, GDB, MGD, and the Entrez Map Viewer. The marker report also lists GenBank and RefSeq records that contain the primer sequences, as determined by Electronic PCR (e-PCR). Marker data, e-PCR and mapping data are availble from the FTP site.

UniSTS integrates marker and mapping data from public resources including GenBank, RHdb, GDB, various human maps (Genethon genetic map, Marshfield genetic map, Whitehead RH map, Whitehead YAC map, Stanford RH map, NHGRI chr 7 physical map, WashU chrX physical map), various mouse maps (Whitehead RH map, Whitehead YAC map, Jackson laboratory's MGD map).

Entrez: The Nucleotides database is a collection of sequences from several sources, including GenBank, RefSeq, and PDB. The number of bases grows at an exponential rate.

!!!Please to see step by step example for using tool in linked page.!!!

Strength and Weakness

This dbSTS has many importance strengths when compare with others database. According to its varieties, nucleotides of many species can be submitted to dbSTS including human, bacterial, viral, pathogens or non-pathogens. And because it’s link within NCBI webpage that allow searcher to easier work with other advantage in NCBI webpage too. So it’s a big and varieties database when compared with other individual or specific database such as “malaria database” that usually provide only information in its field. But dbSTS has weakness in case of deeper detail of each submitted species e.g. malaria database may give more others details of malarial genome than the submitted one in dbSTS. Although dbSTS is a big database of USA but many nucleotides from laboratories around the world may not submitted in dbSTS whereas they may submit their sequence in others database. So dbSTS is not perfect but big and varieties make it more advantage for users.

!!!Please to see step by step example for using tool in linked page.!!!