Listed here are the various programs and databases used by the BASys pipeline to generate genome annotations. These programs and databases are updated over time. A copy of this file appears with your annotation report for your reference.
Programs
| Program | Comments |
|---|---|
| Perl Version 5.8.1 | http://www.perl.org |
| Bioperl 1.4 | http://www.bioperl.org |
| NCBI BLAST 2.2.22 built on Feb 3, 2010 | http://www.ncbi.nlm.nih.gov/BLAST/ |
| Glimmer 2.1.3 |
Glimmer is a popular, fast and highly accurate ab initio gene finding program for microbial DNA. It is used as the main gene finding program at The Institute for Genomic Research (TIGR) for microbial DNA sequencing projects. On a study of for 31 complete bacterial and archaeal genomes, Glimmer achieved an average gene prediction accuracy of 99.36%. Glimmer uses Interpolated Markov Models to distinguish coding regions from non-coding DNA. Glimmer's performance decreases with increasing GC Content. For genomes with high GC content (>60%), Glimmer may generate a high number of false positive predictions and therefore should be used with caution. http://www.tigr.org/software/glimmer/ |
| HMMER 2.3.2 | Used for local Pfam Searches hmmer.wustl.edu/ |
| Homodeller 2.0 | Locally developed homology modelling program. http://redpoll.pharmacy.ualberta.ca/homodeller/ |
| SignalP 3.0 | Signal peptide prediction. http://www.cbs.dtu.dk/services/SignalP/ |
| TMHMM 2.0 | Prediction of transmembrane helices in protein. http://www.cbs.dtu.dk/services/TMHMM/ |
| PSIPRED 2.45 | Secondary structure prediction. PSIPRED achieves an average Q3 score of 80.6% for secondary structure prediction. http://bioinf.cs.ucl.ac.uk/psipred/ |
| ps_scan built on 10/26/2004 | Tool for local PROSITE scans. ftp://us.expasy.org/databases/prosite/tools/ps_scan/ |
| VADAR 1.4 | Locally developed protein structure analysis tool. BASys uses VADAR to analyze protein structures for secondary structural informaton http://redpoll.pharmacy.ualberta.ca/VADAR/ |
| PSORT-B 2.0.4 | Used to predict subcellular location. PSORT-B attains a precision of 96% for Gram-positive and Gram-negative bacteria http://www.psort.org/psortb/index.html |
| ProteinNameExtractor 1.0 | BASys function prediction module. This module was validated against a set of expertly annotated proteins from C.trachomatis. |
| FindParalogs 1.0 | BASys module for paralog identification. The paralogs database is created from the conceptual translations for the identified coding regions supplied to BASys by Glimmer or by the submitter. |
| FindHomologs 1.0 | BASys module for homolog identification. Searches model organism databases for possible homologs. |
| GOSearch 1.0 | BASys module for extracting Gene Ontology information from various sources. |
| OperonFinder 1.0 | BASys module for identifying operons. Based on [2]. |
| StructureManager 1.0 | BASys module for manipulating protein structure files. |
| StructureClassifier 1.0 | BASys module for determining structure class from secondary structure information. |
| Structure Finder 1.0 | BASys module for generating protein structures from various sources. |
| COG_Finder 1.0 | BASys module for identifying COG functional categories and accessions |
| Secondary Structure Manager 1.0 | BASys module for generating secondary structure information from various sources. |
| ECNumber_Finder | BASys module for mapping EC_number to and from various sources. |
| SwissProt Annotation Manager 1.0 | BASys module for comparing and transitively applying annotations from SwissProt records. |
| CCDB Annotation Manager 1.0 | BASys module for comparing and transitively applying annotations from CCDB records. |
| Gene Identifier 1.0 | BASys module for coordinating gene identification information from glimmer or user submissions |
| BASys Annotation Manager 1.0 | The BASys pipeline manager. |
| KEGG Search Manager | BASys module for searching and extracting metabolic information from KEGG. |
| SubCellLocalization Manager 1.0 | BASys module for generating subcellular location annotation from various sources. |
| VADAR Manager 1.0 | BASys module for controlling and parsing VADAR output. |
| BASys Annotation | BASys module for storing annotations and related information (evidence, quality, datestamps, etc.) |
| BASys Stats | BASys module for generating pI, molecular weight, etc. |
| TargetDB Finder | BASys module for searching and extracting status and availability information from the TargetDB database |
Databases
| Database | Last Update |
|---|---|
| NCBI non-redundant database of bacterial protein sequences | January 18, 2012 |
| SwissProt | January 18, 2012 |
| RefDB protein sequences for H. sapiens | January 18, 2012 |
| RefDB protein sequences for C. elegans | January 18, 2012 |
| RefDB protein sequences for D. melanogaster | January 18, 2012 |
| RefDB protein sequences for C. cerevisiae | January 18, 2012 |
| CCDB | Dec 11, 2004 |
| Gene Ontology Maps | November 10, 2009 |
| PDB Database Sequences | November 10, 2009 |
| PDB Database Structures | November 10, 2009 |
| PROSITE | November 10, 2009 |
| Target DB | Novermber 10, 2009 |
| KEGG | November 10, 2009 |
| COG | November 10, 2009 |
References
- Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J. (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci U S A., 97:6652-6657.
- Bendtsen JD, Nielsen H, von Heijne G, Brunak S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340:783-795.
- Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J. (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci U S A., 97:6652-6657.
| BASys version 1.0. |
