Is there any script/program available to compare two gene models (gff and fasta format) generated by gene prediction tools? So what I want as an out put is some comparative statics saying common genes , uniq genes of each set and overlapping genes from two or more gene models.
Thank you in advance
There is a small utility for reporting feature overlaps between gff files.
It requires a bit of editing (sed-ing rather) of typical gff files:
gff file: it should contain at least 8 fields separated by tabs, followed by a list of attributes of the form [key space value] separated by spaces. There should not be any space at the end
sed 's/[;=]/ /g' filename.gff
does the job. I just started testing it (works on my test files) but did not figured out complete usage.
it works well. I didn't understand very well about the mode flag (except boolean overlap) . Could you please give some eg? I am using some sed commands in order to make some conclusion like how many genes structures are identical between two sets. Is that also possible by any flag.
it works well, thank you. I didn't understand very well about the mode flag (except boolean overlap) . Could you please give some eg? I am using some sed commands in order to make some conclusion like how many genes structures are identical between two sets. Is that also possible by any flag.
My understanding is that it does not have a clue about what is being compared. This means that if one gff file contains multiple types (colum3) and other is having i.e. just blast_match, the overlaps will still be reported. If one has 2 files with at least partially matching types, I guess only after grepping and creating temporary files one can get overlaps between desired types.
Yet another gene prediction comparison software, Eval from Brent lab:
http://mblab.wustl.edu/software/eval/
Works OK on provided .gtf example files, giving a very detailed output. Gets confused by gff3 files from Augustus and SNAP, does not seem to understand exonerate output reformatted to gff3. Takes a long time to load Augustus 1.4M lines gff file.
I believe the answer you are looking for is ParsEval, which is now part of AEGeAn software toolkit. This is by some of the same folks who made GAEVAL.
There is some rather old Java program for comparing prediction accuracy: http://bioinformatics.oxfordjournals.org/content/19/13/1712.abstract
ftp://iubio.bio.indiana.edu/molbio/genefind/
I had no time to test it yet.
GFPE runs OK with examples, but it will require at least some GFF file changes to compare AUGUSTUS to exonerate. Re reliable annotation: not exactly. What we need is some kind of estimation how set A compares to set B. Getting numbers like "number of correct / missing / wrong exons" plus "Correlation Coefficient" gives clues about how many exons predicted by A are also predicted by B etc.
The developers of PlantGDB developed a GAEVAL tool (Gene Annotation Evaluation), but this basically scores gene models based on aligned evidence.
I am currently running a genome annotation pipeline and I would like to do the same thing--compare the predictions from the annotation pipeline with the annotations provided by the group that did the sequencing and assembly. I wasn't really interested in Jigsaw, since it takes the two (possibly) disparate gene models and builds a consensus gene model. I'm more interested in what you mentioned--summary statistics about the differences between the two sets of annotations.
I am currently working on a script to do this comparison. I'm still trying to figure out what comparisons/statistics are interesting (borders of gene model, exon agreement, etc). Will share when I have something reliable.
There is JIGSAW, which reads GFF. It does somewhat more than you're asking and combines the input into new gene models.
The reason I mentioned it is that it does the hard work of comparing the gene models. That's not easy, except in the simple case when two models are identical. It does produce some comparative stats on the input gene finders too, but they are totals of genes and exons found/missed etc.
I didn't understand very well about the mode flag . Could you please give some examples? I am using some sed commands in order to make some conclusion like how many genes structures are identical between two sets. Is that also possible by any flag.
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version 2.3.6
Welcome to the (almost) same boat... Do you have proper gene models or a rather messy mixture of gff-s from i.e. exonerate, GMAP, PASA, AUGUSTUS?
Thanks. I have models from Augustus and exonerate