Hello,
projects like the OMIM database allow to find, given a character, information concerning the loci involved in the generation of its phenotype in human.
I would like to know about possible ways to do the reserve search: given a sequence (not necessarily genic), how to find (if any) known phenotypes.
Of course one can do literature search, and also use gene names (just for genic sequences, though) to query databases (including OMIM), but I was looking for a more sequence-oriented tool, something that in principle could be, for example, easily displayed as a custom track.
Hope the question is clear enough, thanks in advance.
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Anima Mundi
There is a mapping phenotype->gene available at: $ curl -s "http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_phenotype_to_genes.txt"
$ curl -s "http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_phenotype_to_genes.txt" | head
#Format: HPO-ID<tab>HPO-Name<tab>Gene-ID<tab>Gene-Name
HP:0001459 1-3 toe syndactyly 2737 GLI3
HP:0006088 1-5 finger complete cutaneous syndactyly 64327 LMBR1
HP:0010708 1-5 finger syndactyly 64327 LMBR1
HP:0010713 1-5 toe syndactyly 2737 GLI3
HP:0000878 11 pairs of ribs 10013 HDAC6
HP:0000878 11 pairs of ribs 3930 LBR
HP:0000878 11 pairs of ribs 6662 SOX9
HP:0000878 11 pairs of ribs 100151683 RNU4ATAC
HP:0000878 11 pairs of ribs 545 ATR
get a file chrom/start/end/geneid from biomart/ensembl . Sort + join both file on Gene-Id: you'll get a BED file with the phenotypes that you can use as a custom-track.
Thanks Pierre; still I welcome suggestions, especially regarding non-genic sequences' annotations, anyway your answer is really helpful.
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