[Genome] help

Fri Jul 27 15:17:50 PDT 2007

Hello Wensheng,

	Hiram and I have been talking about the best way for you to solve your 
problem.  Those EST IDs are quite old (pre human-assembly), and are not 
all present in the latest assembly (hg18).

	ESTs aren't necessarily associated with a single gene.  If you are 
interested in learning what gene (or genes) your ESTs overlap with, you 
can intersect the positional information of your ESTs with a gene track.

	To do this, find the positions of your ESTs and create a custom track. 
  Then you can intersect this custom track with a gene track such as the 
RefSeq Gene track.  The only drawback of this approach is that you will 
lose the EST ID by the time you do the intersection.  To work around 
this problem you can use the Galaxy tool set.  Galaxy has a set of tools 
for performing these types of actions.  They also have a proxy server 
straight to the UCSC Table Browser.  You can find the Galaxy website 
here:  http://main.g2.bx.psu.edu/

	Good luck in your work.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

wzhang19 at umd.edu wrote:
> It was published in
> 
> http://genome-www.stanford.edu/serum/fig2data.txt
> 
> Wensheng
> 
> 
> ---- Original message ----
>> Date: Fri, 27 Jul 2007 13:52:49 -0700
>> From: Ann Zweig <ann at soe.ucsc.edu>  
>> Subject: Re: [Genome] help  
>> To: wzhang19 at umd.edu
>> Cc: genome at soe.ucsc.edu
>>
>> Hello Wensheng,
>>
>> 	I'm sorry that you were not able to get results from the Table Browser. 
>>  I took a look at your list of accession numbers.  I do not recognize 
>> those as GenBank IDs.  Where did you get those accessions?
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>> wzhang19 at umd.edu wrote:
>>> Hello, every one,
>>>
>>> I am conducting a simulation study on the data in Lyer et al (1999). I want to retrieve the gene names from GeneBank accession IDs. But I can not get result from running the Table Browser according to the instruction. Attached is the list. Can you give me a help? Thanks.
>>>
>>>
>>> Wensheng Zhang, PhD
>>> Department of Animal and Avian Science
>>> University of Maryland, College park
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> W95909
>>> AA045003
>>> AA044605
>>> W88572
>>> AA029909
>>> AA059077
>>> AA035657
>>> AA044619
>>> W89012
>>> H19324
>>> N22392
>>> AA027277
>>> W89018
>>> N32247
>>> T62968
>>> H28360
>>> H16592
>>> W78151
>>> R45687
>>> H14500
>>> R81336
>>> N47974
>>> N75026
>>> R87731
>>> H26264
>>> H61274
>>> N63445
>>> W69445
>>> R60336
>>> N53427
>>> H15535
>>> R60731
>>> AA029408
>>> AA018444
>>> AA031778
>>> R49183
>>> W89002
>>> W86006
>>> AA037007
>>> H93791
>>> AA011682
>>> R46079
>>> H05133
>>> N38765
>>> AA057433
>>> N52170
>>> R71462
>>> R60996
>>> R05458
>>> T90846
>>> R59736
>>> N50955
>>> H65598
>>> R24284
>>> H61694
>>> H01236
>>> N74313
>>> H85971
>>> AA025721
>>> AA034939
>>> W45327
>>> N26801
>>> AA036987
>>> W88788
>>> W84708
>>> W80742
>>> AA029996
>>> N95180
>>> W72188
>>> W80746
>>> H66595
>>> AA053461
>>> AA026808
>>> W91979
>>> W79450
>>> H52219
>>> AA037718
>>> AA012996
>>> N33221
>>> N91268
>>> N20862
>>> AA055558
>>> AA047641
>>> AA025786
>>> AA053028
>>> AA040872
>>> AA057199
>>> AA047419
>>> W90080
>>> AA040147
>>> AA036947
>>> N32165
>>> AA043938
>>> W67250
>>> AA029774
>>> N66765
>>> AA024914
>>> T65590
>>> N21470
>>> AA031314
>>> AA034054
>>> AA044633
>>> AA011218
>>> AA029205
>>> W95464
>>> W04611
>>> R38619
>>> R33609
>>> AA039640
>>> W70150
>>> AA042944
>>> W74140
>>> N38985
>>> N64669
>>> T72562
>>> N66534
>>> H29047
>>> R51510
>>> H00168
>>> AA024606
>>> R56644
>>> H62361
>>> R82488
>>> H63779
>>> R15989
>>> R43846
>>> R43729
>>> N70450
>>> AA005169
>>> AA025310
>>> N51744
>>> W93694
>>> H83658
>>> N63574
>>> N79778
>>> N64209
>>> N72289
>>> W71999
>>> AA019203
>>> W81522
>>> AA057771
>>> AA045742
>>> AA029451
>>> H25014
>>> H62473
>>> W45726
>>> AA007609
>>> AA035285
>>> W93986
>>> AA001025
>>> AA045561
>>> AA059074
>>> N67978
>>> AA007439
>>> H17482
>>> N93862
>>> W67226
>>> AA011388
>>> W45465
>>> AA010624
>>> N64806
>>> N50448
>>> N31484
>>> N63511
>>> H08856
>>> W92305
>>> H63374
>>> R44177
>>> N69835
>>> AA045506
>>> AA004712
>>> W93502
>>> AA054129
>>> W87769
>>> N75545
>>> AA025835
>>> AA010407
>>> AA056431
>>> AA058747
>>> AA021607
>>> H86088
>>> N47794
>>> AA016001
>>> N73953
>>> H05758
>>> AA018594
>>> W74533
>>> N72130
>>> N79013
>>> H77631
>>> R70903
>>> R44858
>>> H06287
>>> R43550
>>> H92076
>>> N39221
>>> R73580
>>> R62600
>>> H14569
>>> H88517
>>> T89077
>>> H29270
>>> R43139
>>> N72115
>>> H92461
>>> W46792
>>> W47204
>>> N67806
>>> N63536
>>> H20847
>>> AA040156
>>> N80164
>>> R37278
>>> AA011444
>>> AA043103
>>> T98860
>>> AA024845
>>> AA035360
>>> AA046042
>>> AA056199
>>> R09377
>>> H11911
>>> H15273
>>> W15407
>>> N66980
>>> AA028136
>>> R51896
>>> N68337
>>> N22858
>>> N62692
>>> AA044425
>>> H27880
>>> R39117
>>> AA013256
>>> N33510
>>> N67562
>>> N98485
>>> AA039882
>>> W73942
>>> AA052967
>>> W73157
>>> AA026909
>>> AA026182
>>> AA052933
>>> R00824
>>> H07905
>>> AA025275
>>> AA005212
>>> AA045111
>>> R05666
>>> T63170
>>> N36415
>>> H12318
>>> T91987
>>> T91093
>>> R55334
>>> T91871
>>> N78949
>>> W04525
>>> R55773
>>> W88695
>>> H17413
>>> W73148
>>> AA046654
>>> T40920
>>> T93776
>>> R37986
>>> T40987
>>> R12563
>>> H70783
>>> W86869
>>> AA055521
>>> AA041382
>>> AA004918
>>> AA026761
>>> AA043362
>>> AA026678
>>> AA026314
>>> AA025313
>>> AA039466
>>> AA029995
>>> AA025800
>>> AA053173
>>> W74235
>>> AA045739
>>> AA041403
>>> AA045181
>>> AA045480
>>> AA045372
>>> AA039663
>>> AA046719
>>> H09359
>>> AA016305
>>> AA047080
>>> AA054956
>>> AA033790
>>> AA045283
>>> AA021163
>>> W68000
>>> H65122
>>> H04812
>>> R67964
>>> AA009683
>>> N68268
>>> AA025540
>>> N93426
>>> N54485
>>> W90493
>>> W01871
>>> AA037511
>>> R43551
>>> W93537
>>> W93122
>>> R51770
>>> AA057170
>>> AA045331
>>> AA034524
>>> AA035263
>>> N89934
>>> AA029677
>>> W73785
>>> N55327
>>> W79392
>>> W72759
>>> N53767
>>> T52152
>>> R40626
>>> R10992
>>> H68298
>>> AA004517
>>> T48153
>>> N93479
>>> AA001916
>>> R43728
>>> H29274
>>> W86618
>>> AA041468
>>> AA053076
>>> W74500
>>> H94471
>>> AA010065
>>> N90191
>>> R39436
>>> AA004917
>>> AA041370
>>> AA058863
>>> T95837
>>> R20750
>>> H27557
>>> N22386
>>> T70079
>>> R40776
>>> R16980
>>> AA045438
>>> T50056
>>> W72836
>>> AA053239
>>> R39209
>>> AA024572
>>> T77817
>>> AA004694
>>> W47101
>>> W45324
>>> R26543
>>> H52671
>>> N93284
>>> W74492
>>> AA057727
>>> AA053251
>>> AA045836
>>> H11257
>>> AA039310
>>> H26271
>>> H24396
>>> AA057068
>>> H96519
>>> T48819
>>> R48580
>>> AA007419
>>> R78403
>>> W51763
>>> T62835
>>> H02832
>>> R59865
>>> AA037156
>>> N79533
>>> AA009609
>>> W52295
>>> W44678
>>> H02191
>>> T40595
>>> T89996
>>> T79471
>>> AA053556
>>> AA057638
>>> AA056414
>>> H23544
>>> N22383
>>> AA056583
>>> AA031961
>>> AA031267
>>> AA028950
>>> N91825
>>> AA056621
>>> AA056338
>>> N71362
>>> AA052965
>>> AA055578
>>> AA043796
>>> T54874
>>> R16047
>>> W46577
>>> AA056401
>>> N63308
>>> AA037351
>>> N40987
>>> AA057780
>>> AA020014
>>> R99596
>>> R39465
>>> AA029292
>>> N74406
>>> AA052986
>>> R78226
>>> H01822
>>> AA044617
>>> N32784
>>> AA043969
>>> AA026141
>>> H72904
>>> W74639
>>> N49296
>>> W44416
>>> AA053331
>>> N47476
>>> AA045473
>>> AA054706
>>> R53619
>>> AA058543
>>> N67200
>>> W86798
>>> AA032091
>>> AA045437
>>> N73309
>>> N93476
>>> W84538
>>> H72723
>>> W19191
>>> N98463
>>> AA046701
>>> AA053259
>>> AA044444
>>> AA039313
>>> AA037369
>>> W73776
>>> N80129
>>> AA037443
>>> N35315
>>> T89175
>>> N23200
>>> H85111
>>> H73480
>>> H77597
>>> N55459
>>> R42883
>>> H88808
>>> W49619
>>> N69996
>>> H48459
>>> AA007629
>>> R21832
>>> R21877
>>> AA017446
>>> AA057761
>>> AA053249
>>> AA058324
>>> W67134
>>> AA001722
>>> AA059125
>>> AA046749
>>> AA046659
>>> AA046721
>>> AA035527
>>> AA042891
>>> AA040861
>>> W49706
>>> N90531
>>> R36703
>>> R49309
>>> R34833
>>> R80217
>>> W46413
>>> N94487
>>> AA045731
>>> AA057667
>>> AA044993
>>> AA056549
>>> N58770
>>> N23941
>>> AA057826
>>> W42606
>>> AA026120
>>> AA034912
>>> N99070
>>> AA044235
>>> R77289
>>> AA047266
>>> H11003
>>> N98591
>>> AA045715
>>> AA057359
>>> AA055585
>>> AA016304
>>> AA013396
>>> W88807
>>> W90037
>>> W88650
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Genome maillist  -  Genome at soe.ucsc.edu
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome