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INTRODUCTION Our users, from Biologic department, want to use HMMER and InterProScan by an easy way saving processing time. –Graphic User Interface instead of command line interface. –They are few users that submit many jobs ( ). –Submit jobs with files upper than 10 MB. –Reduce the processing time using other computers. –Depend of the job, the time could be 1 h to 12 h. –Some jobs from InterProScan fail, and must be submited again.
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PORTING HMMER AND INTERPROSCANTO THE GRID
Daniel Alberto Burbano Sefair (dburbano@uniandes.edu.co) Michael Angel Pérez Cabarcas (mic-pere@uniandes.edu.co)
University of The AndesInformation Technology Division
ColombiaNovember 2008
Topics
• Introduction• HMMER• InterProScan• What do we have?• What do we want with your help?• Questions
INTRODUCTION
• Our users, from Biologic department, want to use HMMER and InterProScan by an easy way saving processing time.
– Graphic User Interface instead of command line interface.– They are few users that submit many jobs (1000 - 3000).– Submit jobs with files upper than 10 MB.– Reduce the processing time using other computers.– Depend of the job, the time could be 1 h to 12 h.– Some jobs from InterProScan fail, and must be submited again.
1. What is HMMER?- “HMMER is a sequence analysis tool using profile Hidden Markov Models”.- It is a set of 9 applications used by command line:
hmmpfam, hmmsearch, hmmalign, hmmbuild, hmmconvert, hmmcalibrate, hmmemit,
hmmindex, hmmfetch.
The above definition is taked from: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/Userguide.pdf
Home page: http://hmmer.janelia.org/
HMMERProfile Hidden Markov Models
2. How can I use HMMER by command, PBS, and JDL?HMMER is a command line application, this is an example
hmmsearch file.hmm MySequence.fasta >> output
HMMER
1. What is InterProScan?
The following definition is taked from Europan Bioinformatic Institute: http://www.ebi.ac.uk/2can/tutorials/function/InterProScan.html
“InterProscan is a tool that combines different protein recognition methods into one resource. It scans a given protein sequence against the protein signatures of the InterPro member databases (PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMMs.”
Home Page: http://www.ebi.ac.uk/Tools/InterProScan/
InterProScan
2. How does InterProScan work?
1. The User submit a protein sequence.
2. Protein sequence applications are launched and search against specific databases.
3. Each application returns a list of hits.
4. The results are combined.5. The information returned to
the user
1
2 3
4
InterProScan
Infomration and Sshema are taken from: http://www.ebi.ac.uk/2can/tutorials/images/scan_schema.gif
3. How can I use InterProScan by command, PBS, and JDL?
InterProScan is a command line application, this is an example
iprscan -cli –I input.seq -o test.out -format raw -goterms -iprlookup
InterProScan
What do we have?
• Bioinformatic Grid Wrapper (BGW) for HMMER and InterProScan that is a Command Line Interface (CLI)
What do we want with your help?
Architecture
Thanks
?
• “Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.”
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