FirstEF pipeline

FirstEF specifications


Unique identifier OMICS_14907
Name FirstEF
Alternative name First Exon Finder
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A DNA sequence, the cutoff value parameters, user’s email address.
Input format FASTA
Output data The predicted exon and relative data.
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Michael Zhang <>

Publication for First Exon Finder

FirstEF citations

PMCID: 2527337

[…] genome. we used the ucsc liftover tool to convert riken's hg17 human genome coordinates to the more recent hg18 genome. our final line of evidence was ab initio promoter predictions generated by the firstef program [23]., each line of evidence identifies a transcription start site (tss). we considered tsss separated by > 500 bp to be distinct promoters – a commonly used criterion. although […]

PMCID: 1273639

[…] gene types. †number of all transcripts of this type., *method 0 used original firstef alone to predict promoters in the upstream and genic regions of these genes. †method 1 used de novo firstef to predict promoters in the upstream and genic regions of these genes. ‡method 2 compared mrnas or predicted transcripts with original firstef predictions to filter out promoters […]

FirstEF institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
FirstEF funding source(s)
This work was supported by grants from the National Institutes of Health and by a CSHL Association fellowship.

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