Introduction of NLM Databases

2. Introduction of NLM Databases dbEST Expressed Sequence Tag Database S.MohammadZad & M. Safari; Graduate Students of MLIS

3. WHAT IS dbEST?(Expressed Sequence Tags) • The EST database is a collection of short single-read transcript sequences from GenBank. • These sequences provide a resource to evaluate gene expression,find potential variation, and annotate genes. • for sequences (usually partial and single-pass) of messenger RNA (i.e., cDNA derived from mRNA) • Note that you can search non-human, non-mouse ESTs separately EST Database

4. dbEST... • The sequences submitted to dbEST were created from thousands of different cDNA libraries and may have originated from whole organs (for example, human brain and liver), specialized tissues, or individual cells • Sequences in dbEST have been submitted by various EST sequencing projects and are freely available. EST Database

5. dbEST... • Since 1992, when the first EST data appeared in GenBank, the number of EST sequences has dramatically increased. • As of July 2008, dbEST contained more than 54 million sequences (from about 22 000 libraries) and accounts for nearly 62% of all GenBank entries EST Database

6. WHO USE EST? • Genetic Engineers • Biotechnologist • Bioinformatics Engineers • And all peopel related to this topic EST Database

7. Ways to Access dbESTData • available from NCBI by anonymous ftp and through Entrez. • The nucleotide sequences may be searched using the BLAST electronic mail server. BLAST: Basic Local Alignment Search Tool • EST sequences are also available as a flat file in the FASTA format by anonymous ftp in the ftp://ftp.ncbi.nih.gov/repository/dbEST/ EST Database

8. http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/iupac_aa_abbreviations.htmlhttp://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/iupac_aa_abbreviations.html EST Database

9. EST Database

10. WHAT ARE EST SECTIONS? EST Database

11. HOW IS EST’s USING? How do I use a simple query? • You can use a protein name,gene name,or gene symbol directly. • Searching with a submitter or author name in the following format will produce the best results. Smith JR (last name followed by initials, no punctuation) • Database identifiers such as accession numbers or gi numbers will directly retrieve the full sequence record. CAA79696 • To find a match to an exact phrase, enclose it in quotation marks. "contactin associated protein" EST Database

12. HOW IS EST’s USING?... • Use the Boolean operator to find better records • Use the Limits page to select the appropriate limit & Restrict your search to specific subsets of records (such as specific organism, molecule type, source database, genomic or cDNA library name) • You can also use the Filter your results after a search. • You can change the format, number, or sorting order of records with Display Settings menu • For download sequence records,Click the Send to menu EST Database

13. :For example EST Database

14. :For example EST Database

15. QUESTION & ANSWER EST Database

16. For Group Work با استفاده از پایگاه اطلاعاتی EST پاسخ سوال زیر را پیدا کنید: • How do I analyze the sequence data directly or find additional related data? • Contactin • neurofascin EST Database

17. ANSWER: EST Database

18. Thank You for Your Attention EST Database