[BioPython] UniGene parser
Sagar Damle
sagar@caltech.edu
Tue, 16 Jul 2002 16:43:50 -0700
Hi cayte,
the unigeneparser looks simple in design and works just right. I have a couple of suggestions, though they're not all that interesting and are probably more my personal preference.
- make a list out of the cDNA sources (['heart', 'lung', 'placenta'])
- under table 'selected model' separate column 2 & 3 values into a list (in the printout, I can't tell if you're already doing this)
In general, I guess, make rows with more than 1 value column, a list of values in the tabledictionary.
- change 'see also' tablename to something more intuitive ('links'?)
sagar
On Tue, 16 Jul 2002 18:53:17 -0700
"Cayte" <katel@worldpath.net> wrote:
> I just did some experiments with LocusLink files and when I strip out the
> html tags very little information is left.
> For this reason I think I should use the same approach as UniGene. Have you
> checked out Record in
> Unigene? Is this what you want?
>
> Cayte
>
key EST SEQUENCES
key is AA101851
cDNA clone IMAGE:489768 Uterus 5' read 2.0 kb
key is AA102060
cDNA clone IMAGE:489768 Uterus 3' read 2.0 kb
key is AA938640
cDNA clone IMAGE:1574076 Kidney 3' read 1.8 kb
key is R82654
cDNA clone IMAGE:149308 Placenta 3' read 2.4 kb
key is R82703
cDNA clone IMAGE:149308 Placenta 5' read 2.4 kb
key EXPRESSION INFORMATION
key is SAGE
Gene to Tag mapping
key is cDNA sources
Brain, CNS, Colon, Germ Cell, Heart, Kidney, Lung, Muscle, Ovary, Pancreas, Parathyroid, Placenta, Pooled, Prostate, Stomach, Testis, Tonsil, Uterus, Whole embryo, cervix, colon, head_neck, lung, muscle, nervous_normal, ovary, pancreas, uterus
key MAPPING INFORMATION
key is Chromosome
3
key is Cytogenetic Position
3q13.3
key is UniSTS entries
1765
A004F36
stSG42984
key SEE ALSO
key is HomoloGene
Hs.13225
key is LocusLink
8702
key is OMIM
604015
key SELECTED MODEL
key is C. elegans
PID:g3880435- similar to n-acetyllactosamine synthase39 % / 217 aa
key is D. melanogaster
PID:g4972702- unknown41 % / 277 aa
key is H. sapiens
PID:g3132900- beta-1,4-galactosyltransferase100 % / 343 aa
key is M. musculus
PID:g3869131- beta-1,4-galactosyltransferase II51 % / 262 aa
key is R. norvegicus
PID:g3258653- UDP-Gal:glucosylceramide beta-1,4-galactosyltransferase43 % / 262 aa
key UniGene Cluster
Hs.13225
key mRNA/GENE SEQUENCES
key is AB024436
Homo sapiens mRNA for beta-1,4-galactosyltransferase IV, complete cds
key is AF022367
Homo sapiens beta-1,4-galactosyltransferase mRNA, complete cds
key is AF038662
Homo sapiens chromosome 3q13 beta-1,4-galactosyltransferase mRNA, complete cds
key is AK001006
Homo sapiens cDNA FLJ10144 fis, clone HEMBA1003286, highly similar to Homo sapiens mRNA for beta-1,4-galactosyltransferase IV