Question: Tools To Visualise Genomic Sequence-Associated Phenotypes In Human
0
gravatar for Anima Mundi
5.8 years ago by
Anima Mundi2.5k
Italy
Anima Mundi2.5k wrote:

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.

ADD COMMENTlink modified 5.8 years ago by Pierre Lindenbaum124k • written 5.8 years ago by Anima Mundi2.5k
1
gravatar for Pierre Lindenbaum
5.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

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.

ADD COMMENTlink written 5.8 years ago by Pierre Lindenbaum124k

Thanks Pierre; still I welcome suggestions, especially regarding non-genic sequences' annotations, anyway your answer is really helpful.

ADD REPLYlink written 5.8 years ago by Anima Mundi2.5k
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