jvarkit

Gff3UpstreamOrf

Takes a ucsc genpred file, scan the 5’ UTRs and generate a GFF3 containing upstream-ORF. Inspired from https://github.com/ImperialCardioGenetics/uORFs

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar gff3upstreamorf  [options] Files

Usage: gff3upstreamorf [options] Files
  Options:
    --break-original-orf
      if ATG(uORF) is in frame with original ORF , do not calculate the 
      peptide beyond the original ATG.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
  * -r, -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --strength
      only accept events that are greater or equal to this Kozak strength.
      Default: nil
      Possible Values: [Strong, Moderate, Weak, nil]
    --version
      print version and exit

Keywords

• gff
• gff3
• uorf
• uorf

Creation Date

20220724

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/upstreamorf/Gff3UpstreamOrf.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite gff3upstreamorf ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

inspiration

Part of this code was inspired from: https://github.com/ImperialCardioGenetics/uORFs/blob/master/5primeUTRannotator/five_prime_UTR_annotator.pm

Wikipedia:

An Upstream Open Reading Frame (uORF) is an open reading frame (ORF) within the 5’ untranslated region (5’UTR) of an mRNA. uORFs can regulate eukaryotic gene expression. Translation of the uORF typically inhibits downstream expression of the primary ORF. In bacteria, uORFs are called leader peptides, and were originally discovered on the basis of their impact on the regulation of genes involved in the synthesis or transport of amino acids.

Examples

Example 1

 java -jar dist/gff3upstreamorfasta  -R GRCh38.fa Homo_sapiens.GRCh38.107.chr.gff3.gz > uorf.gff3

note to self: test ENSG00000141736 https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003529

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