Genome completion status
Tracking genome projects is difficult
Which metazoan species currently have genomic data available? That's hard to say -- it's a difficult process to track. There are no announcements, maintained lists, or publications; sequencing centers rarely update their websites or indicate specific future plans. Consequently few researchers are adequately aware of what species have genomic data, and so typically undersample when doing comparative genomics projects. Sampling species more densely often overturns working hypotheses of feature evolution.
Tracking Sanger reads
Sequencing centers post raw trace reads on a day-by-day basis at NCBI's trace archives. NCBI performs some quality control and adds them to the accruing database that is blastn accessible. Later the center may assemble them into contigs and post them to the "wgs" division of GenBank (more rarely at "gss" or "htgs"). Depending on the coverage and finishing effort, these contigs can be hosted as a genome by a browser center such as UCSC. It may take 2-3 years for data to complete its migration from trace sequencing to contigs to genome. More rarely, traces are withheld and a genome assembly appears abruptly, as with elephantfish.
Further complications include multiple subspecies for gorilla, orang and gibbon, personal human genomes, diploid genomes, areas of confused taxonomy (alpaca vs vicuna) and so on. NISC and sequencing centers do not always work from same individual animal or even same subspecies so each trace compilation has to be checked separately. Transcript programs can use yet other individual animals or subspecies.
To annotate at kbp scales (adequate for exons and small genes), one can reliably use the traces or contigs and not wait (years) for a genome browser to appear.
If the exon or feature is 1000 bp (or in such pieces), the trace archives work quite well, especially for establishing presence. Absence is not as informative because data might simply be missing due to low coverage. No vertebrae species is truly complete yet including human. it requires a few million traces before a given incoming genome is worth checking for a given feature.
Not every trace makes it into a contigs or assembly -- singletons are often omitted, often millions of them. Sequencing often continues after a release, as is happening now with elephant and guinea pig. Consequently the trace archive at NCBI is always the resource of last resort, ie if a feature is missing from assembled traces, it is best to go back to the trace archive because all original data is there. However NCBI posting of traces to its blast database can lag trace inputs from the sequencing centers by a week or more, which can amount to 1.5 million traces in an active project.
There are also "cdna" species like the marsupial, Trichosurus vulpecular, which have rather complete coverage of coding genes but no genome project underway. Such sequences can furnish critical close-in query material to improve the sensitivity of trace blast (which is not sensitive at any evolutionary distance if the feature is evolving rapidly).
In a concrete comparative genomics research project, it is important to document which species were considered. For that it is convenient to enter annotation data in a column next to its species, in a spreadsheet containing all species with genomic data (provided below and illustrated below that with a concrete coding indel example). This allows last-minute updating prior to paper submission.
Finally, PCR can be used on species currently lacking genomic or cdna projects when it is critical to augment sampling density. Flying lemur would be a good choice in primate-oriented projects because it appears to be the immediate outgroup (hence a great improvement over distant mouse).
Two recent papers illustrate these concepts and explain methods of contemporary comparative genomics in greater detail:
Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ. Molecular and genomic data identify the closest living relative of primates. Science. 2007 Nov 2;318(5851):792-4. PMID: 17975064 Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 2007 Apr;17(4):413-21. PMID: 17322288
Available genome assemblies as of May 2008
The table is correct as of 01 May 08. Traces indicated in millions, eg Trc12 means 12 million traces but no wgs contigs or assembly available Wgs08 means wgs division of GenBank contains short assembled contigs searchable with tBlastn Mar06 etc means the March 2006 assembly is the most recent available at UCSC Mar06 homSap Homo sapiens (human) Mar06 panTro Pan troglodytes (chimp) Trc04 gorGor Gorilla gorilla (gorilla) Jul07 ponPyg Pongo pygmaeus (orang_abelii) Trc19 nomLeu Nomascus leucogenys (gibbon) Jan06 macMul Macaca mulatta (rhesus) Trc12 papHam Papio hamadryas (baboon) Trc17 tarSyr Tarsius syrichta (tarsier) Jun07 calJac Callithrix jacchus (marmoset) Dec06 otoGar Otolemur garnettii (bushbaby) Wgs08 micMur Microcebus murinus (mouse_lemur) Trc00 cynVol Cynocephalus volans (flying_lemur) Dec06 tupBel Tupaia belangeri (treeshrew) Jul07 musMus Mus musculus (mouse) Nov04 ratNor Rattus norvegicus (rat) Wgs08 speTri Spermophilus tridecemlineatus (ground_squirrel) Trc07 dipOrd Dipodomys ordii (kangaroo_rat) Wgs08 cavPor Cavia porcellus (guinea_pig) May05 oryCun Oryctolagus cuniculus (rabbit) Wgs08 ochPri Ochotona princeps (pika) May05 canFam Canis familiaris (dog) Mar06 felCat Felis catus (cat) Aug06 bosTau Bos taurus (cow) Trc10 turTru Tursiops truncatus (dolphin) Trc06 susScr Sus scrofa (pig) Trc11 vicVic Vicugna vicugna (vicugna) Jan07 equCab Equus caballus (horse) Wgs08 myoLuc Myotis lucifugus (microbat) Trc08 pteVam Pteropus vampyrus (macrobat) Wgs08 sorAra Sorex araneus (shrew) Wgs08 eriEur Erinaceus europaeus (hedgehog) May05 loxAfr Loxodonta africana (elephant) Trc09 proCap Procavia capensis (hyrax) Jul05 echTel Echinops telfairi (tenrec) May05 dasNov Dasypus novemcinctus (armadillo) Trc09 choHof Choloepus hoffmanni (sloth) Trc10 macEug Macropus eugenii (wallaby) Jan06 monDom Monodelphis domestica (opossum) Mar07 ornAna Ornithorhynchus anatinus (platypus) May06 galGal Gallus gallus (chicken) Trc15 taeGut Taeniopygia guttata (finch) Feb07 anoCar Anolis carolinensis (lizard) Aug05 xenTro Xenopus tropicalis (frog) Jul07 danRer Danio rerio (zebrafish) Oct04 takRub Takifugu rubripes (fugu) Feb04 tetNig Tetraodon nigroviridis (pufferfish) Feb06 gasAcu Gasterosteus aculeatus (stickleback) Apr06 oryLat Oryzias latipes (medaka) Wgs08 calMil Callorhinchus milii (elephantfish) Mar07 petMar Petromyzon marinus (lamprey)
A coding indel example (a coding exon from gene SPC25 on human chr2) illustrates the usefulness of multiple genomes in timing and understanding evolution of insertions and deletions.
homSap MVEDELALFDKSINEFWNKFKST--DTSCQMAGLRDTYKDSIKAFA panTro MVEDELALFDKSINEFWNKFKST--DTSCQMAGLRDTYKDSIKAFA ponPyg MVEDELALFDKSINEFWNKFKST--DTSCQMAGLRDTYKDSIKAFA macMul MVEDELALFDKSINEFWNKFKST--DTSCQMAGLRDTYKDSIKAFA calJac MVEDELALFDKSLNEFWNKFKST--DTTFQMAGLRDTYKDSLKAFA tarSyr MVEDELTLFDKSINEFWNKFKST--DTANQMMGLRDTYKDSVKAFA otoGar MVEDQLALLDKNINEFWNKFKST--DTAGQMAGLRDTYKDSIKTFA micMur MVEDELVLFDKTVNEFWNKFKST--DTSCHMVGLRDTYKDSLKAFA cynVol .................NKFTST--DTSCQMMGLRGTNK....... tupBel MVEDELALFDKGINEFWNKFRSTVSDTSCQMVGLRDAYKDSIKAFA musMus MGEDELALLNQSINEFGDKFRNRLDDNHSQVLGLRDAFKDSMKAFS ratNor MGEDELAAFEKSINEFGDKFRYRLSDNRSQVLGLKDAFKDSIRALS cavPor MVEDELALFDKSINEFGNKFRNTLSDTPCQMLGLRDACKDSIKTLA speTri MMEDELARFDKSINEFGNKFRNTFSDTRCQMVGLRDVFKDSIEALA dipOrd MVEDELAHFDKSISEFGSKFRNTLSDTPSQTVGLRDAYKDSIKALS oryCun MVEDELALFDKSINEFGSKFRSTLSDAPCQMVGLRDAYKDSVKSLT ochPri MVEDELALFDKSINEFGSKFRSTLSDTPCQMVGLREACKDSVRLLT canFam MIDDELAQFDKSISEFWSKFKGTVSDTSSQMVGLRETYKDSIKACA felCat MIEDELALFDKSINEFWNKFKSTLSDTSCQMMGLRDTYKDSIKALT equCab MVEDELALFDKSINEFWNKFKNTVSDTSCQMVGLRDAYKDSIKAFA myoLuc MVEDELALLDKNINEFWNKFKSNVNDTSCQMVGLRDNYKDISKAFT pteVam MVEDELALLDKSINEFWNKFKSSVSDTSCQMMALRDSYKDINKAFT bosTau MVEDELALFDKSINEFWNKFKSTVSDTSCQMVGLRETYKDSIKAFA turTru MVEDELALFDKSINEFWNKFRSTVSDTSCQMVGLRDTYKDSIKAFA susScr MVEDELALFDKSINEFWNRFKSTVSDTSCQMVGLRENYKDSLKAFA oviAri MVEDELALFDKSLNEFWNKFKSTVNDTSCQMVGLREAYKDSIKAFA eriEur MVEDELALFDKSINEFWNKFKGTVSDTSFQMVGLRDTYKDSIKIFT sorAra MVEDELVLFEKSINEFVNEFESTASDTTCQVVGPRDADKDSIKALA dasNov MIEDELALFDKSINEFWNKFKGTVSDNSCQMVGLRDTYKDSIKAFA choHof MIEDELALFDKSINEFWNKFKSAVSDTSCQMVGLRDTYKDSIKAFA loxAfr MIEDELVQFDKSINEFWNKFINTASDTSCQMVGLRDAYKDSMKAFA proCap MIEDELRQFDKSINEFWNKFINTTSDTSCQMAGLRDAYKDSMKAFA echTel MIEDELLQFDKSMNEFRNKHFNTLNDTSGQMMGLRDTYRDSMKAFA monDom MSHIKTEEELDLFNKSINDFWNKFRNTTLNEHCSQMVGLRDTYKDSIEALT macEug MSHIKTEEELDIFEKSISDFWNRFRNTAFNEPYSQVVGVRDTYKYSIETLT triVul MSHIKTEEELDIFNKSINDFWNRFRNTTFNEHYSQVVGLRDTYKNSIEALT ornAna MSHIKTEEELALFDKSIDEFWTKFKNTWISEYSCQTVTLRDAHKEAIKALT galGal MSAVKTEDEITVVEREMKEFWTELKSVYGTEQINQTLALRDSCKESINVLS taeGut MGNAQAEDEVALFEKDMKEFWIQFKISYGTEQNNQTMKEFWIQFKISYGTE anoCar MAKAKEEDELTMLEKGIEELCTQIETTYCRQSLEKTSGPRNKCYKSGPRNK
Live blog of an actual exon recovery session:
I updated the available chordate genomes today and their practical access. Pig contigs were released a couple days ago ... they are stored at the HTG division of GenBank and various other inconvenient places. The existing 28-way can be boosted to a 32-way using the net tracks for lamprey, lancelet, marmoset, and orangutan. That can be boosted to a 37-way bringing in Microcebus, Spermophilus, Ochotona, Myotis, and Callorhinchus using a single tBlastn of the wgs division of GenBank using the new capability of boolean species restriction. The 51-way then requires individual queries at the trace archives.
Mark D suggested an interesting trick (which I've amended): set the browser to its 5000 pixel maximum as needed, open in pdf view, scrape off amino acid lines as text, remove spaces and equal signs, watch out for nucleotides also in caps and extraneous symbols, paste into a new column of the ss below in default sort order. If an exon is fairly well-behaved in the comp genomics sense, that provides it for species in the 28-way that have it.
Net tracks have to be opened individually and translated (or uBlastx'ed against fiducial). As always, the trace archives has to be consulted at the end to fill in any residual gaps because millions of singletons get left out of assemblies.
To illustrates what happens in real life (ie the difficulty of fully automating the process proteomewide), I looked an exon of MAN1A2. The 28-way gave 25 sequences, with a proximal frameshift in eriEur and nothing for tupBel and dasNov. eriEur had two covering traces and the browser contig had taken the wrong one; tupBel had one trace coverage with 6 frameshifts, unusable. Armadillo has gone to 6x lately and trace coverage was excellent.
The net tracks yielded compelling ponPyg and petMar translations but nothing for braFlo and a calJac implausibly with two indels. However calJac at the trace archives had indel-free coverage with the expected conservation; the browser again was hosting a contig assembly error or bizarre polymorphism.
Wgs searching restricted to 'Microcebus OR Spermophilus OR Ochotona OR Myotis OR Callorhinchus' avoids a results page swamped out with sequences already on hand. It still takes forever because so many genomes have been placed in this db. The search here provides a good outcome for all but speTri where only a paralogous exon match occurs. speTri had the needed coverage in the trace archives however. Sometimes the paralog story and other anomalies only emerge from an alignment of all the collected sequences at the end.
It's also worth checking est_others for ad hoc species. Here it's best to look at the taxonomy sort-page. I picked up susScr and papHam, stubbing in Papio anubis for the latter. Another 6 species were available should it later prove mission-critical to flesh out certain regions of the tree:
Echis ocellatus ............. 77 1 hit [snakes] Bothrops jararaca ........... 70 1 hit [snakes] Gekko japonicus ............. 70 1 hit [lizards] Ambystoma mexicanum ......... 77 1 hit [salamanders] Squalus acanthias ----------- 74 1 hit [sharks and rays] Leucoraja erinacea .......... 70 3 hits [sharks and rays]
By using this method of descending quality and convenience, only 12 individual searches at the trace archives are needed. This protein is evolving slowly enough that a single fixed nucleotide blastn query will suffice, either human, boreoeuthere, or reconstructed ancestor. Because the pulldown menu contains hundreds of species, the ones sought should be queried in alphabetic order to simplify sequential setting of the target species. That process took 14 minutes here to get 9 additional species, ending up with a 46-way on this exon or a 52-way using the 6 transcript species above.
In summary, enough data is out there to double up on what the browser 28-way offers. The downside is that even after optimizing the process it takes an hour or more per exon. In this project, I'm looking at non-synonymous changes in 100 exons in the first fully sequenced extinct species. There will have to be some prioritization early on, but this can be based on analysis of the initial pdf screenscrape.
col1 species order if scraping protein off the 'Conservation' 28-way, by net availability, otherwise by declining trace reads col2 species phylogenetic order, sister leafs subordered by assembly quality col3 assembly, wgs contig, htg contigs, trace archives (last two digits show millions of reads) col4 6-letter genSpp code col5 genus col6 species col7 common and subspp 1,1,>,Mar06,homSap,Homo,sapiens,(human) 2,2,>,Mar06,panTro,Pan,troglodytes,(chimp) 3,6,>,Jan06,macMul,Macaca,mulatta,(rhesus) 4,10,>,Dec06,otoGar,Otolemur,garnettii,(bushbaby) 5,13,>,Dec06,tupBel,Tupaia,belangeri,(treeshrew) 6,14,>,Jul07,musMus,Mus,musculus,(mouse) 7,15,>,Nov04,ratNor,Rattus,norvegicus,(rat) 8,18,>,Wgs08,cavPor,Cavia,porcellus,(guinea_pig) 9,19,>,May05,oryCun,Oryctolagus,cuniculus,(rabbit) 10,30,>,Wgs08,sorAra,Sorex,araneus,(shrew) 11,31,>,Wgs08,eriEur,Erinaceus,europaeus,(hedgehog) 12,21,>,May05,canFam,Canis,familiaris,(dog) 13,22,>,Mar06,felCat,Felis,catus,(cat) 14,27,>,Jan07,equCab,Equus,caballus,(horse) 15,23,>,Aug06,bosTau,Bos,taurus,(cow) 16,35,>,May05,dasNov,Dasypus,novemcinctus,(armadillo) 17,32,>,May05,loxAfr,Loxodonta,africana,(elephant) 18,34,>,Jul05,echTel,Echinops,telfairi,(tenrec) 19,38,>,Jan06,monDom,Monodelphis,domestica,(opossum) 20,39,>,Mar07,ornAna,Ornithorhynchus,anatinus,(platypus) 21,42,>,Feb07,anoCar,Anolis,carolinensis,(lizard) 22,40,>,May06,galGal,Gallus,gallus,(chicken) 23,43,>,Aug05,xenTro,Xenopus,tropicalis,(frog) 24,44,>,Jul07,danRer,Danio,rerio,(zebrafish) 25,46,>,Feb04,tetNig,Tetraodon,nigroviridis,(pufferfish) 26,45,>,Oct04,takRub,Takifugu,rubripes,(fugu) 27,47,>,Feb06,gasAcu,Gasterosteus,aculeatus,(stickleback) 28,48,>,Apr06,oryLat,Oryzias,latipes,(medaka) 29,50,>,Mar07,petMar,Petromyzon,marinus,(lamprey) 30,51,>,Mar06,braFlo,Branchiostoma,floridae,(lancelet) 31,9,>,Jun07,calJac,Callithrix,jacchus,(marmoset) 32,4,>,Jul07,ponPyg,Pongo,pygmaeus,(orang_abelii) 33,11,>,Wgs08,micMur,Microcebus,murinus,(mouse_lemur) 34,16,>,Wgs08,speTri,Spermophilus,tridecemlineatus,(ground_squirrel) 35,20,>,Wgs08,ochPri,Ochotona,princeps,(pika) 36,28,>,Wgs08,myoLuc,Myotis,lucifugus,(microbat) 37,49,>,Wgs08,calMil,Callorhinchus,milii,(elephantfish) 38,25,>,Htg08,susScr,Sus,scrofa,(pig) 39,5,>,Trc19,nomLeu,Nomascus,leucogenys,(gibbon) 40,8,>,Trc17,tarSyr,Tarsius,syrichta,(tarsier) 41,41,>,Trc15,taeGut,Taeniopygia,guttata,(finch) 42,7,>,Trc12,papHam,Papio,hamadryas,(baboon) 43,26,>,Trc11,vicVic,Vicugna,vicugna,(vicugna) 44,37,>,Trc10,macEug,Macropus,eugenii,(wallaby) 45,24,>,Trc10,turTru,Tursiops,truncatus,(dolphin) 46,36,>,Trc09,choHof,Choloepus,hoffmanni,(sloth) 47,33,>,Trc09,proCap,Procavia,capensis,(hyrax) 48,29,>,Trc08,pteVam,Pteropus,vampyrus,(macrobat) 49,17,>,Trc07,dipOrd,Dipodomys,ordii,(kangaroo_rat) 50,3,>,Trc04,gorGor,Gorilla,gorilla,(gorilla) 51,12,>,Trc00,cynVol,Cynocephalus,volans,(flying_lemur)
Final fasta output >homSap Mar06 Homo sapiens (human) MAN1A2 exon AIEKYCRVNGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >panTro Mar06 Pan troglodytes (chimp) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >gorGor Trc04 Gorilla gorilla (gorilla) AIEKYRRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >ponPyg Jul07 Pongo pygmaeus (orang_abelii) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETL >nomLeu Trc19 Nomascus leucogenys (gibbon) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >macMul Jan06 Macaca mulatta (rhesus) AIEKYCRVTGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >papHam Trc12 Papio hamadryas (baboon) AIEKYCRVNGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >tarSyr Trc17 Tarsius syrichta (tarsier) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >calJac Jun07 Callithrix jacchus (marmoset) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >otoGar Dec06 Otolemur garnettii (bushbaby) AIEKYCRVTGGFSGIKDVYSSVPTHDDVQQSFFLAETLK >micMur Wgs08 Microcebus murinus (mouse_lemur) AIEKYCRVSGGFSGIKDVYSSTPTHDDVQQSFFLAETLK >cynVol Trc00 Cynocephalus volans (flying_lemur) - >tupBel Dec06 Tupaia belangeri (treeshrew) -- >musMus Jul07 Mus musculus (mouse) AIEKSCRVSGGFSGVKDVYAPTPVHDDVQQSFFLAETLK >ratNor Nov04 Rattus norvegicus (rat) AIEKSCRVSGGFSGVKDVYSPTPAHDDVQQSFFLAETLK >speTri Wgs08 Spermophilus tridecemlineatus (ground_squirrel) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >dipOrd Trc07 Dipodomys ordii (kangaroo_rat) - >cavPor Wgs08 Cavia porcellus (guinea_pig) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >oryCun May05 Oryctolagus cuniculus (rabbit) AIEKHCRVRGGFSGIKDVYSSTPTHDDVQQSFFLAETLK >ochPri Wgs08 Ochotona princeps (pika) AIEKHCRVRGGFSGIKDVYSSTPTHDDVQQSFFLAETLK >canFam May05 Canis familiaris (dog) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >felCat Mar06 Felis catus (cat) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >bosTau Aug06 Bos taurus (cow) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >turTru Trc10 Tursiops truncatus (dolphin) AIEKYCRVTGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >susScr Htg08 Sus scrofa (pig) ALEKHCRVNGGYSGLRDVYVSAQTYDDVQQSFFLAETLK >vicVic Trc11 Vicugna vicugna (vicugna) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >equCab Jan07 Equus caballus (horse) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >myoLuc Wgs08 Myotis lucifugus (microbat) AIEKYCRVSGGFSGVKDVYSSTPAHDDVQQSFFLAETLK >pteVam Trc08 Pteropus vampyrus (macrobat) AIEKYCRVSGGFSGVKDVYSSTPAHDDVQQSFFLAETLK >sorAra Wgs08 Sorex araneus (shrew) AIEKYCRVSSGFSGVKDVYSSTPTHDDVQQSFFLAETLK >eriEur Wgs08 Erinaceus europaeus (hedgehog) AIEKYCRVSSGFSGVKDVYSSTPTHDDVQQSFFLAETLK >loxAfr May05 Loxodonta africana (elephant) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >proCap Trc09 Procavia capensis (hyrax) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLK >echTel Jul05 Echinops telfairi (tenrec) AIEKYCRVSGGFSGVKDVYSSTPTHDDVQQSFFLAETLk >dasNov May05 Dasypus novemcinctus (armadillo) AIEKNCRVSSGFSGVKDVYSANPTHDDVQQSFFLAETLK >choHof Trc09 Choloepus hoffmanni (sloth) AIEKYCRVSSGFSGVKDVYSSNPTHDDVQQSFFLAETLK >macEug Trc10 Macropus eugenii (wallaby) - >monDom Jan06 Monodelphis domestica (opossum) AIEKYCRVRGGFSGIKDVYSSAPAYDDVQQSFFLAETLK >ornAna Mar07 Ornithorhynchus anatinus (platypus) AIEKSCRVSGGFSGVKDVYSSAPAYDDVQQSFFLAETLK >galGal May06 Gallus gallus (chicken) AIDKYCRVSGGFSGVKDVYSSSPTYDDVQQSFFLAETLK >taeGut Trc15 Taeniopygia guttata (finch) AIDKYCRVSGGFSGVKDVYSSSPTYDDVQQSFFLAETLK >anoCar Feb07 Anolis carolinensis (lizard) AIDKYCRVSGGFSGVKDVYSSAPTFDDVQQSFFLAETLK >xenTro Aug05 Xenopus tropicalis (frog) AIDKYCRVSGGFSGIKDVYSSSPTYDDVQQSFFLAETLK >danRer Jul07 Danio rerio (zebrafish) ALEKHCRVEGGYSGVRDVYSNNPNHDDVQQSFYLAETLK >takRub Oct04 Takifugu rubripes (fugu) AIDKYCRVSGGFSGVKDVYSSNPTYDDVQQSFFLAETLK >tetNig Feb04 Tetraodon nigroviridis (pufferfish) AIDKYCRVSGGFSGVKDVYSSSPTYDDVQQSFFLAETLK >gasAcu Feb06 Gasterosteus aculeatus (stickleback) AIDKYCRVSGGFSGVKDVYSSNPTYDDVQQSFFLAETLK >oryLat Apr06 Oryzias latipes (medaka) AIDKYCRVSGGFSGVKDVYSSNPTYDDVQQSFFLAETLk >calMil Wgs08 Callorhinchus milii (elephantfish) AIDKYCRVIGGFSGVKDVYSSTPAYDDVQQSFFLAETLK >petMar Mar07 Petromyzon marinus (lamprey) ALEKYCRVEGGFSGIRDVYSSSPAHDDVQQSFFLAETLK >braFlo Mar06 Branchiostoma floridae (lancelet) -
Tracking 454 reads
These six transcript projects are the pick of the 454 litter as of May 2008 in terms of vertebrate data. Transcripts have a lot more payload being coding than random genomic snippets in terms of alignability and ease of working with. The file sizes are very reasonable, considering how much data is in them. These are fasta-formatted sequence data only, compressed but not encoded in any way and in the public domain. Read quality is separately available but probably of less interest to most biomedical researchers.
homSap SRA000297 Homo sapiens Transcriptome Study 454 GS FLX WUGSC don't need calJac SRA000144 Callithrix jacchus Transcriptome Study WUGSC tupBel SRA000295 Tupaia belangeri Transcriptome Study 454 GS FLX WUGSC ornAna SRA000294 Ornithorhynchus anatinus Transcriptome Study 454 GSFLX WUGSC tacAcu SRA000241 Tachyglossus aculeatus Transcriptome Study 454 GS FLX WUGSC galGal SRA000238 Gallus gallus Transcriptome Study 454 GS FLX WUGSC
