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ProGlycProt Tutorial

Access and analyze glycoprotein sequence data using five different tools for search, entry comparison, and blast. Retrieve information on ProGPdb, ProGTdb, search by features, structure gallery, and links.

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ProGlycProt Tutorial

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  1. ProGlycProt Tutorial 2nd Release

  2. Home Page Information can be retrieved by clicking on any of the desired links appearing as pull-down menus under five headings – ProGPdb, ProGTdb, Search by Features, Structure Gallery and Links Click on any of the five different tools that have been developed for glycoprotein sequence analysis, entry comparison and blast. Facilitates an interactive database search using select features displayed on left side of the map Displays statistics of a particular subcategory within each section of the database This References section shows the papers published on the database

  3. How to search the ProGPdb section Place the cursor on ProGPdb or ProGTdband select from the pull-down menu appearing thereafter Example Display Page will give you an idea of the type of information existing for a given entry Small window for searching ProCGP and ProUGP

  4. How to search the ProCGP or ProUGP sections for a glycoprotein entry Select either ProCGP or ProUGP at a given time Select any requisite search criterion among the list Select any desired value from the list generated corresponding to the previously selected search criterion Select either All or a particular display criterion about which the information is required Click Click on any ID to get the result page displayed

  5. How to search the ProGTdb section for a glycosyltransferase entry Example Display Page will give you an idea of the type of information existing for a particular entry Small window for searching ProGT (Main and Accessory sections) Search for any given glycosyltransferase antry in the Main or Accessory sections in the same way as shown in the previous slide for ProGPdb

  6. How to search all sections by Features Select any sub-section while searching for a particular entry

  7. How to search Structure Gallery Place the cursor Place the cursor All homology models corresponding to either ProCGP or ProGT are displayed upon click Search by organism name All crystal structures corresponding to either ProCGP or ProGT are displayed upon click Click here Search by ProGP or ProGT ID

  8. How To Look For Recent Reviews, Related Tools & Databases And Bibliography Reviews Bibliography Tools and Databases Click to see the review in PubMed Click to see the reference in PubMed Click to open the tools or databases

  9. How To Use Map Sequon Tool? Paste protein sequence in fasta format Visual display of specified glycosite sequons in a protein sequence Click submit

  10. How To Use GlySeq Extractor Tool? Paste protein sequence Select a sequence window. -5 to +5 is set by default. Select a glycosite pattern. NX(S/T) is set by default. Click to display pull-down menu Click submit Extracted sequences around the selected glycosite pattern

  11. How To Use Predict Glycosite Tool? Select prediction programme- either for N-linked or O-linked glycosylation prediction Click submit to yield results Select threshold from the pulldown menu

  12. How To Use Compare Tool? Select the section from which the entries are to be compared Select display criteria from the pulldown menu Select the entries to be compared from the pulldown menu Click to compare upto four different glycoproteins or GTs

  13. How To Use BLAST Tool? Paste a protein sequence in fasta format Select weight matrix. BLOSUM62 is set by default. Select expect value in the pull-down menu. 1 is set by default. Blast result page Select the section against which the blast is to be run Click Run Blast

  14. How To Use Map View Feature For Interactive Database Search Alternative Search- Click here Select database section- ProGPdb, ProGTdb main or accessory Select organism name from the pulldown menu Select subcellular location Select glycosylation type Glyco Group location on map is displayed after entering any ProGP or GT ID Upon selection of criteria, the location of the corresponding Glyco-Group is displayed on the map

  15. Look For Database Statistics

  16. Other Features Click on the questions about the database to see their answers

  17. Typical Result Page 1 Click to open the links

  18. Typical Result Page 2

  19. Typical Result Page 3

  20. Typical ProGT Result Page 1

  21. Typical ProGT Result Page 2

  22. Typical ProGT Result Page 3

  23. Typical ProGT Result Page 4

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