HMAP

From Informatics

• What labs or how many are using HMAP?

  - Honig lab

• Who is the main “database authority” for HMAP?

  - Kely Norel (rn98<at>columbia.edu)

• What kind of database is it? (flat-file, relational, XML, etc)

  - flat-file

• Size of database?

  ~ 29,000 templates

• Anticipated yearly growth? (Megabytes/Gigabytes)

- difficult to predict

• Backup procedures? How often?
• Database backups (Hot, Cold, Both) [and/or]
• Operating system backup

  - OS backup

• What servers/operating systems are hosting them (IP addresses)

• IP = 156.145.30.88 > vesta
• Red Hat Enterprise Linux AS release 4 (Nahant Update 3)

• Approximately how many *active* users?

- number of users in the Honig lab ~ 15

• How often is the database used? (Daily, Weekly, Monthly)

- daily

• What platforms are being used? (Oracle, MySQL, PostgreSQL, etc)

  - N/A

• What applications are using these databases?
• Web interface?
• Application (GUI)?
• Command line interface (CUI)?

• SCOP and PRISM are used by HMAP

• Is it accessible from outside the firewall to public users?

  - no

• What is the primary purpose of the database & types of data stored?

  • HMAP is a method for hybrid multidimensional alignment of profiles which combines sequence, secondary and tertiary information in protein structures into profiles to facilitate the detection of remote homologs and perform sequence-to-sequence alignments
  • It alternately uses sequence and structural information in different regions (loop/motif/core) according to patterns that reflect the global topology of the protein as well as regions that have significant local sequence signals
  • This server is built with the principle of providing a searchable database for users to find and align remote sequence homologs
  • The database for HMAP contains approximately 13,000 templates, which are 90% sequence non-redundant. They comprise SCOP domains as well as full chains. Each template contains at least 30 residues.

• Are there any issues or problems with the database?
• Specific error messages popping up?
• Problems connecting from the application or web interface?
• Performance issues (queries are slow, freezes at times, etc)

• - no, runs smoothly

• Would they like help in administering the database?

• - no

• What additional features or changes would users like to see?
• new tables or queries
• additional screens on application or web interface
• migrate to different database platform (i.e. MySQL to Oracle)

• none at the moment