Hi Tom, Thank you for all of your detailed feedback and suggestions. We are adding these items to our tracking system. Our engineers will be in contact with you if they have any questions or responses for you.
-- Brooke Rhead UCSC Genome Bioinformatics Group On 12/2/11 9:07 AM, thomas pringle wrote: >> donnaK A request -- when you notice things are broken on our site >> (such as your comment about gator + crocodile blat), could you make >> sure to report those to us right away so we can check into them? A >> brief email to [email protected] will do the trick. I've asked >> the browser project mgr (Ann Zweig) to check into some of the >> items > > Hi folks, > > Below are some suggested bug fixes for the blat page at genome-test > (and elsewhere): > > -1- put the list of targets into phylogenetic order, as induced by > human on top and usefulness within subclade (eg mouse on top of > rodents). see modified menu below > > -2- use a consistent notation throughout: Genus species (common). no > abbreviations. no acronyms. no capitalization of species name (eg > Takifugu Rubripes). , no circular stuff like S. cerevisiae > (Saccharomyces cerevisiae), no disease name in place of genus-species > (eg malaria). Many visitors are not American and know the scientific > name but not the common names. > > -3- follow through consistently with Genus species (common) at top of > blat page, on blat result page, on browser page reached by blat, and > on genomes page reached from browser page. > > -4- blat result page should carry chromosome:start-stop coordinates > of match and link to browser. right now it just carries the > chromosome but not the range and is simply top-of-page navigation (we > all have page-up and home keys). > > -5- assembly should be defaulted to most recent assembly (eg fugu > uses oct 04 instead of oct 11), even if older versions have more > tracks. It would be better if assemblies were not a pulldown but > instead had all choices visible as radio buttons. [[people are going > to use the default, not check all the versions for all their tracks, > not even realize other assemblies are available.]] > > -6a- blat is too weak. It needs an option to bump the sensitivity on > protein blat: "BLAT on proteins finds sequences of 80% and greater > similarity of length 20 amino acids or more. In practice DNA BLAT > works well on primates, and protein blat on land vertebrates." In > other words, you can't use a human query to find the counterpart in > zebrafish. It can't find short exons even when they are exact matches > and internal to a longer hit. > > -6b- even if blat is strengthened, all deuterostome genomes should > minimally contain the human protein blast track. this is only > available erratically. the big advantage is human HUGO gene names > enables successful text searching in the browser coord window. > > -6c- blast gateway page into all available genomes (most recent > assembly). This can be made available the day the genome is released, > thus ahead of building blat page or browser. More on this shortly. > > -7a- Reconcile browsers with blats. Makes no sense to have a browser > like Jan 2011 tilapia (Oreochromis niloticus) with no blat entry > point and no human HUGO gene name gateway. There are quite a few of > these. They too are way out of phylogenetic order (see re-numbering > below). > > 1 J. Craig Venter 2 Baboon 4 Bushbaby 5 Mouse lemur 6 Tree shrew 11 > Shrew 7 Squirrel 8 Pika 12 Hedgehog 10 Megabat 9 Dolphin 3 Tarsier 13 > Rock hyrax 6.5 Kangaroo rat 15 Wallaby 14 Tenrec > > > -7b- lack of consistency: the browser genomes page shows species > grouped by 'clade' but blat menu does not. Organizing by clade is a > good idea. Maybe this should be called 'Group' instead -- Ancestor, > Haplotype and Simulation are not clades. Vertebrates is not a clade > either but rather a clade-complement so maybe 'Other Vertebrates'. > Vertebrates and Deuterostomes (whose number will always be very > small) could be consolidated into 'Other Deuterostomes'. Insects > should be Arthropods to allow room for expansion. 'Other' should be > reordered as shown below (and fixed as above for latin name) > > Mammal Vertebrate Deuterostome Insect Nematode Ancestor Other > Haplotypes Simulation > > Sea hare Sea anemone Plasmodium (malaria) Yeast Saccharomyces > cerevisiae MMTV Mouse Mammalian Tumor Virus SARS coronavirus > > -8- how is A H1N1 different from H1N1 A, are these still being used, > not working today. suggest that they be dropped as of interest > yesteryear. > > -9- Insects and nematodes need to be in correct order. this requires > literature searchin when GenBank taxonomy only provides polytomies. > > -10- Here are the new and old menu orders, tab-delimited db > > Menu Old New Genus species (common) GRCh37.p5 1 1 > Homo sapiens > GRCh37.p5 (human) GRCh37.p2 2 2 Homo sapiens > GRCh37.p2 (human) Human > 3 3 Homo sapiens hg19 (human) Chimp 4 4 Pan > troglodytes (chimp) > Gorilla 5 5 Gorilla gorilla (gorilla) Orangutan 6 > 6 Pongo abelii > (orangutan) Gibbon 7 7 Nomascus leucogenys > (gibbon) Rhesus 8 8 Macaca > mulatta (rhesus) Marmoset 9 9 Callithrix jacchus > (marmoset) Mouse 12 > 10 Mus musculus (mouse) Rat 13 11 Rattus > norvegicus (rat) Guinea pig > 14 12 Cavia porcellus (guineapig) Rabbit 15 13 > Oryctolagus cuniculus > (rabbit) Cat 16 14 Felis catus (cat) Panda 17 15 > Ailuropoda > melanoleuca (panda) Dog 18 16 Canis familiarus (dog) > Horse 19 17 > Equus caballus (horse) Microbat 20 18 Myotis > lucifugus (microbat) Pig > 21 19 Sus scrofa (pig) Cow 22 20 Bos taurus > (cow) Sheep 23 21 Ovis > aries (sheep) Boreoeutherian 40 22 Boreoeuthere Sloth 24 > 23 Choloepus > hoffmanni (sloth) Armadillo 25 24 Dasypus novemcinctus > (armadillo) > Elephant 26 25 Loxodonta africana (elephant) > Opossum 27 26 > Monodelphis domestica (opossum) Platypus 28 27 > Ornithorhynchus > anatinus (platypus) Chicken 29 28 Gallus gallus > (chicken) Turkey 30 > 29 Meleagris gallopavo (turkey) Zebra finch 31 30 > Taeniopygia guttata > (finch) American alligator 52 31 Alligator mississippiensis > (alligator) Saltwater crocodile 50 32 Crocodylus porosus > (crocodile) > Lizard 32 33 Anolis carolinensis (lizard) X. tropicalis > 33 34 Xenopus > tropicalis (frog) Zebrafish 34 35 Danio rerio > (zebrafish) Tetraodon > 35 36 Tetraodon nigroviridis (pufferfish) Fugu 36 > 37 Takifugu > rubripes (fugu) Stickleback 37 38 Gasterosteus > aculeatus > (stickleback) Medaka 38 39 Oryzias latipes (medaka) Lamprey > 39 40 > Petromyzon marinus (lamprey) C. intestinalis 42 41 Ciona > intestinalis > (tunicate) C. savignyi 43 42 Ciona savignyi > (tunicate) Lancelet 41 43 > Branchiostoma floridae (amphioxus) S. purpuratus 44 44 > Strongylocentrotus purpuratus (urchin) D. melanogaster 58 > 45 > Drosophila melanogaster (fruitfly) D. simulans 59 46 > Drosophila > simulans (fruitfly) D. sechellia 60 47 Drosophila > sechellia > (fruitfly) D. yakuba 61 48 Drosophila yakuba (fruitfly) D. > erecta 62 > 49 Drosophila erecta (fruitfly) D. ananassae 63 50 > Drosophila > ananassae (fruitfly) D. pseudoobscura 64 51 Drosophila > pseudoobscura > (fruitfly) D. persimilis 65 52 Drosophila persimilis > (fruitfly) D. > virilis 66 53 Drosophila virilis (fruitfly) D. > mojavensis 67 54 > Drosophila mojavensis (fruitfly) D. grimshawi 68 55 > Drosophila > grimshawi (fruitfly) A. gambiae 69 56 Anopheles gambiae > (mosquito) T. > castaneum 71 57 Tribolium castaneum (beetle) A. > mellifera 70 58 Apis > mellifera (bee) C. elegans 45 59 Caenorhabditis elegans > (nematode) C. > brenneri 47 60 Caenorhabditis brenneri (nematode) C. > briggsae 48 61 > Caenorhabditis briggsae (nematode) C. remanei 49 62 > Caenorhabditis > remanei (nematode) C. japonica 51 63 Caenorhabditis japonica > (nematode) H. contortus 57 64 Haemonchus contortus > (nematode) M. > hapla 55 65 Meloidogyne hapla (nematode) M. incognita 56 > 66 > Meloidogyne incognita (nematode) B. malayi 54 67 Brugia > malayi > (nematode) P. pacificus 53 68 Pristionchus pacificus > (nematode) Sea > hare 46 69 Aplysia californica (sea_hare) Malaria 72 > 70 Plasmodium > falciparum (protozoan) S. cerevisiae 73 71 Saccharomyces > cerevisiae > (yeast) A H1N1 10 72 Influenza virus H1N1 A H1N1 A > 11 73 Influenza > virus H1N1 A > > thanks for looking into this! tom > > > > > > > > > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
