DbAccessMsmithPei

DbAccessMsmithPei - Accessing Some Bioinformatics Databases...

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Accessing Some Bioinformatics Databases Pei-Jie Wu 1 Access SRS 1.1 Searching from Google ( www.google.com ) using keyword “SRS6”. 1.2 Directly access http://srs.ebi.ac.uk/ 2 Click on “Start” going to the Top Page of SRS@EMBL-EBI 2.1 This page provides a category of Bioinformatics databases library. ( http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz ) 2.2 We select 4 typical domains database of molecular biology as our example: DNA/RNA sequence, Protein sequence, Protein 3D structure, and Genetic mapping 3 Example 1: EMBL-EBI DNA/RNA sequence database 3.1 Click “DNA/RNA Seq” on the left hand side of the page. 3.2 Enter keyword in dialog window, e.g. insulin. 3.3 The entry page shows up the list of entries relating the keyword. User can click any EMBL indexed entry to see the detail content. 4 Example 2: Protein sequence, we select PIR 4.1 Click “ PIR ” under “Sequence libraries – complete” category. 4.2 Web page shows information summary of PIR. 4.3 Click website address ( http://pir.georgetown.edu/ ) to link to the PIR main page. 4.4 Database Use Case: PIR 4.4.1 PIR: Protein Identification Resource 4.4.2 Protein and nucleic acid sequence databases 4.4.3 Click i ProClass 4.4.4 iProClass: An integrated protein classification database. It provides 3 query methods: text search, BLAST search, and peptide match. 4.4.5 Type “insulin” in text search. 4.4.6 PIR search result lists all entries relating the keyword. User can select any specific entry to get information summary and amino acid sequence. 5 Example 3: Protein 3D structure, we select PDB 5.1 Click “ ” in front of “Protein3Dstruct” to open the content of this category. 5.2 Click “ PDB ” under “Protein3Dstruct”. 5.3 Web page shows information summary of PDB. 5.4 Click website address ( http://www.rcsb.org/pdb/ ) to link to the PDB main page. 5.5
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This note was uploaded on 02/10/2012 for the course CSE 5615 taught by Professor Mitra during the Fall '11 term at FIT.

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DbAccessMsmithPei - Accessing Some Bioinformatics Databases...

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