jvarkit

BackLocate

Mapping a mutation on a protein back to the genome.

Usage

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

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

Usage: backlocate [options] Files
  Options:
  * -g, --gtf
      A GTF (General Transfer Format) file. See 
      https://www.ensembl.org/info/website/upload/gff.html . Please note that 
      CDS are only detected if a start and stop codons are defined.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    -p, --printSeq
      print mRNA & protein sequences
      Default: false
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --version
      print version and exit

Keywords

• vcf
• annotation
• prediction
• protein

See also in Biostars

• https://www.biostars.org/p/15992
• https://www.biostars.org/p/116366
• https://www.biostars.org/p/425422

Creation Date

20140619

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/backlocate/BackLocate.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/backlocate/BackLocateTest.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 backlocate ? 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

Example

mutation P->M at 1090 in NOTCH2

$  echo -e "NOTCH2\tP1090M" | java -jar dist/backlocate.jar -R hg19.fa --gtf ucsc.gtf
(...)
#User.Gene	AA1	petide.pos.1	AA2	knownGene.name	knownGene.strandknownGene.AA	index0.in.rna	codon	base.in.rna	chromosome	index0.in.genomic	exon
##uc001eik.3
NOTCH2	P	1090	M	uc001eik.3	NEGATIVE	P	3267	CCA	C	chr1	120480548	Exon 20
NOTCH2	P	1090	M	uc001eik.3	NEGATIVE	P	3268	CCA	C	chr1	120480547	Exon 20
NOTCH2	P	1090	M	uc001eik.3	NEGATIVE	P	3269	CCA	A	chr1	120480546	Exon 20
##uc001eil.3
NOTCH2	P	1090	M	uc001eil.3	NEGATIVE	P	3267	CCA	C	chr1	120480548	Exon 20
NOTCH2	P	1090	M	uc001eil.3	NEGATIVE	P	3268	CCA	C	chr1	120480547	Exon 20
NOTCH2	P	1090	M	uc001eil.3	NEGATIVE	P	3269	CCA	A	chr1	120480546	Exon 20

$ echo -e "NOTCH2\tPro1090M\tInteresting" | java -jar dist/backlocate.jar --gtf ucsc.gtf -R /path/to/human_g1k_v37.fasta | grep -v "##" | java -jar dist/prettytable.jar 

+------------+-----+--------------+-----+----------------+------------------+--------------+---------------+------------+----------------------+-------------+------------+-------------------+---------+-----------------+
| #User.Gene | AA1 | petide.pos.1 | AA2 | knownGene.name | knownGene.strand | knownGene.AA | index0.in.rna | wild.codon | potential.var.codons | base.in.rna | chromosome | index0.in.genomic | exon    | extra.user.data |
+------------+-----+--------------+-----+----------------+------------------+--------------+---------------+------------+----------------------+-------------+------------+-------------------+---------+-----------------+
| NOTCH2     | Pro | 1090         | Met | uc001eik.3     | -                | P            | 3267          | CCA        | .                    | C           | 1          | 120480548         | Exon 20 | Interesting     |
| NOTCH2     | Pro | 1090         | Met | uc001eik.3     | -                | P            | 3268          | CCA        | .                    | C           | 1          | 120480547         | Exon 20 | Interesting     |
| NOTCH2     | Pro | 1090         | Met | uc001eik.3     | -                | P            | 3269          | CCA        | .                    | A           | 1          | 120480546         | Exon 20 | Interesting     |
| NOTCH2     | Pro | 1090         | Met | uc001eil.3     | -                | P            | 3267          | CCA        | .                    | C           | 1          | 120480548         | Exon 20 | Interesting     |
| NOTCH2     | Pro | 1090         | Met | uc001eil.3     | -                | P            | 3268          | CCA        | .                    | C           | 1          | 120480547         | Exon 20 | Interesting     |
| NOTCH2     | Pro | 1090         | Met | uc001eil.3     | -                | P            | 3269          | CCA        | .                    | A           | 1          | 120480546         | Exon 20 | Interesting     |
+------------+-----+--------------+-----+----------------+------------------+--------------+---------------+------------+----------------------+-------------+------------+-------------------+---------+-----------------+

See also

• http://plindenbaum.blogspot.fr/2011/03/mapping-mutation-on-protein-to-genome.html
• https://github.com/lindenb/jvarkit/issues/14
• https://github.com/lindenb/jvarkit/issues/13

History

• 2019: move to GTF
• 2019: add extra user data
• 2017: Moved to jcommander
• 2014: Moved to jvarkit
• Nov 2014 : removed all the dependencies to SQL and DAS; use a local indexed genome
• Aug 2015 : Added a new column “potention var codon” (as https://twitter.com/_ramrs/status/631123002005061633 ) , renamed “codon” to “wild codon”

Cited in

backlocate was cited in:

• CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations. 2017 Nat Meth. http://dx.doi.org/10.1038/nmeth.4327.
• “Differential 3’ Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types” Sasa Jereb, Hun-Way Hwang, Eric Van Otterloo, Eve-Ellen Govek, John J Fak, Yuan Yuan, Mary E Hatten, Robert B Darnell BioRxiv https://www.biorxiv.org/content/biorxiv/early/2018/01/10/245886.full.pdf

This site is open source. Improve this page.