Tag: EMOTIF

eBAS 3.6 – eMOTIF Batch Analysis Suite

eBAS 3.6

:: DESCRIPTION

eBAS (eMOTIF Batch Analysis Suite permits eMOTIF licensees to analyze groups of proteins or entire proteomes for the presence of eMOTIFs in batch fashion.The core of this software bundle is a Makefile script that has streamlined and automated the steps involved in running the database of eMOTIFS against multiple ORFs, genomes, and proteomes. ebas accepts FASTA-formatted ORF sequences, FASTA-formatted genomic DNA sequences, and FASTA-formatted protein sequences as input. eBAS assumes the ORFs are reported in the right frame; therefore, ebas will only translate one frame of the ORF sequences. Genomic DNA sequences, on the other hand, may or may not code for proteins; ebas, therefore, will translate all six frames of the genomic DNA sequences. The input protein and translated sequences are then piped to eMOTIF-SEARCH for automated classification. ebas has been applied to coding sequences derived from the Arabidopsis thaliana genomic sequence.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C Complier
  • EMOTIF

:: DOWNLOAD

   eBAS

:: MORE INFORMATION

Citation:

Huang, J. Y. and Brutlag, D. L. (2001).
The eMOTIF Database.
Nucleic Acids Research, 29(1), 202-204.

EMOTIF 3.6 – Sequence Analysis Using Pareto-optimal Discrete Motifs

EMOTIF 3.6

:: DESCRIPTION

EMOTIF includes the following three programs:

(1) eMOTIF-SEARCH: Given a protein sequence, the eMOTIF-SEARCH program suggests families of proteins to which the query sequence may belong. The eMOTIF-SEARCH program considers a protein sequence a potential member of a protein family, if the sequence contains discrete motif or motifs that have been generated from an ungapped multiple sequence alignment of known member sequences from that family.

(2) eMOTIF-MAKER: The eMOTIF-MAKER program converts an ungapped multiple sequence alignment into a set of Pareto-optimal discrete motifs for use by the eMOTIF-SEARCH program and the eMOTIF-SCAN program. The resulting set of motifs often reveals sub-families within the cluster of proteins that share the region of sequence similarity covered by the given ungapped multiple sequence alignment.

(3) eMOTIF-SCAN: Given a regular expression, the eMOTIF-SCAN program finds all the occurrences of that regular expression in a particular sequence database.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C Complier

:: DOWNLOAD

  EMOTIF

:: MORE INFORMATION

Citation:

Nevill-Manning, C. G., Wu, T. D. and Brutlag, D. L. (1998).
Highly Specific Protein Sequence Motifs for Genome Analysis.
Proc. Natl. Acad. Sci. May 26, 1998 vol. 95 no. 11 5865-5871