Hi Janeela, You can use the Table Browser again. Select (Clade/Genome/Assembly) Mammal/Pig/susScr2 and:
group: Gene and Gene prediction tracks track: Ensebl Genes (or N-Scan Genes) table: ensGene (or nscanGene) region: genome identifiers (names/accessions): click on "paste list" and paste in the identifiers following the instructions. output format: sequence Click get output Select sequence type: genomic Click Submit On the sequence retrieval options page, make sure to uncheck the Introns box. Other than that the defaults should work for you - just read down the list to make sure, then click Ge Sequence. If you have further questions, please contact us at [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 4/4/11 3:41 PM, janeela khan wrote: > > Thank you so very much. It was very useful information for me. I wonder if I > can also retrieve the exonic sequence for the pig genome?> From: > [email protected] >> Subject: Genome Digest, Vol 99, Issue 3 >> To: [email protected] >> Date: Fri, 1 Apr 2011 12:00:12 -0700 >> >> Send Genome mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Genome digest..." >> >> >> Today's Topics: >> >> 1. Re: help: Exonic position map to Protein position >> (Vanessa Kirkup Swing) >> 2. Re: How to generate mapping between Ensembl and refseq >> transcript IDs (Hiram Clawson) >> 3. Re: bedgraph data will not display points (Hiram Clawson) >> 4. Re: when is a query excessive. (Galt Barber) >> 5. Re: bedgraph data will not display points >> (Lionel (Lee) Brooks 3rd) >> 6. Re: bedgraph data will not display points (Hiram Clawson) >> 7. protein families (Tom Traut) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 1 Apr 2011 09:38:36 -0700 (PDT) >> From: Vanessa Kirkup Swing<[email protected]> >> Subject: Re: [Genome] help: Exonic position map to Protein position >> To: janeela khan<[email protected]> >> Cc: UCSC genome<[email protected]> >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=utf-8 >> >> Hi Janeela, >> >> To figure out where in the exon the protein is translated from, you will >> need to use the table browser. To get to the table browser click on on >> "Tables" from the blue navigation bar. >> >> Set the clade, genome, and assembly. >> >> Then you will need to set the following: >> >> group: Gene and Gene prediction tracks >> track: UCSC Genes >> table: knownGene >> region: genome >> identifiers (names/accessions): click on "paste list" and paste in the >> identifiers following the instructions. >> output format: selected fields from primary and related tables >> >> click "get output" >> >> select the fields you want displayed. >> >> click "get output" >> >> Hope this helps lead you in the right direction. If you have further >> questions, please contact us at [email protected] >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> ----- Original Message ----- >> From: "janeela khan"<[email protected]> >> To: "UCSC genome"<[email protected]> >> Sent: Thursday, March 31, 2011 8:21:24 AM >> Subject: [Genome] help: Exonic position map to Protein position >> >> >> >> Dear All, >> Could you guide me how I can map certain Positions in an exon to the Protein >> positions? Here i donot have the exact genomic positions but I have the gene >> name and the relative position in an exon. Is there a way to map this >> position to protein? >> Thanks for the help in advance >> MvH/janeela >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 01 Apr 2011 09:41:00 -0700 >> From: Hiram Clawson<[email protected]> >> Subject: Re: [Genome] How to generate mapping between Ensembl and >> refseq transcript IDs >> To: "Cook, Malcolm"<[email protected]> >> Cc: "'Rajasimha, Harsha \(NIH/NEI\) \[C\]'"<[email protected]>, >> "'[email protected]'"<[email protected]> >> Message-ID:<[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Sorry Malcolm, there isn't a generic method for all genomes at UCSC. >> This is a most interesting example you have here. Usually chrM at >> Ensembl is: "Mt" >> >> Newer genome assemblies at UCSC are including two tables: >> ensemblLift >> ucscToEnsembl >> >> Which allow translation of UCSC names to Ensembl names and >> coordinate conversions for haplotypes and other random bits that >> might be located in a different coordinate system. For example: >> >> $ hgsql -e "select * from ensemblLift;" hg19 >> +-----------------+----------+ >> | chrom | offset | >> +-----------------+----------+ >> | HSCHR4_1 | 69170076 | >> | HSCHR17_1 | 43384863 | >> | HSCHR6_MHC_APD | 28696603 | >> | HSCHR6_MHC_COX | 28477796 | >> | HSCHR6_MHC_DBB | 28696603 | >> | HSCHR6_MHC_MANN | 28696603 | >> | HSCHR6_MHC_MCF | 28696603 | >> | HSCHR6_MHC_QBL | 28696603 | >> | HSCHR6_MHC_SSTO | 28659142 | >> +-----------------+----------+ >> >> $ hgsql -e "select * from ucscToEnsembl;" hg19 | grep MHC >> chr6_ssto_hap7 HSCHR6_MHC_SSTO >> chr6_qbl_hap6 HSCHR6_MHC_QBL >> chr6_mcf_hap5 HSCHR6_MHC_MCF >> chr6_mann_hap4 HSCHR6_MHC_MANN >> chr6_cox_hap2 HSCHR6_MHC_COX >> chr6_dbb_hap3 HSCHR6_MHC_DBB >> chr6_apd_hap1 HSCHR6_MHC_APD >> >> It would be a useful process to go back over some of the older popular >> genomes to add these conversion tables. >> >> --Hiram >> >> Cook, Malcolm wrote: >>> Hiram, >>> >>> Is there a similar approach for chromosomal identifiers? (i.e. chrM in dm3 >>> is dmel_mitochondrion_genome at ensemble) >>> >>> Or better, an SQL query for same? >>> >>> Thx >>> >>> Malcolm Cook >>> Stowers Institute for Medical Research - Bioinformatics >>> Kansas City, Missouri USA >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 01 Apr 2011 09:49:16 -0700 >> From: Hiram Clawson<[email protected]> >> Subject: Re: [Genome] bedgraph data will not display points >> To: Lionel Brooks<[email protected]> >> Cc: [email protected] >> Message-ID:<[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Good Morning Lionel: >> >> The bedGraph drawing mechanism can construct bar graphs at your >> specified intervals, or when you select graphType=points it will >> draw only the top of the bar graph at your specified intervals. >> There is no line drawing except by the trick of "smoothing" points >> such that they appear to be in a line graph. This only works if >> the data points are continuous when seen in the genome browser. >> Smoothing will not smear points into areas where there is no >> data value specified. >> >> The Genome Graphs function of the genome browser: >> http://genome.ucsc.edu/cgi-bin/hgGenome >> will only draw lines between your specified points. >> >> See also: >> >> http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format >> >> --Hiram >> >> Lionel Brooks wrote: >>> Hello all, >>> >>> I have a bedgraph file. In the past I have used to files to attain >>> graphic output in the form of a smoothed line but I uploaded my most >>> recent data set and now I cannot get a line graph. In fact, I'm not >>> sure what I am looking at because the values that are displayed along >>> the y-axis are not described with a label. >>> >>> Here is my track line: >>> track type=bedGraph autoScale=on graphType=points windowingFunction=mean >>> smoothingWindow=16 >>> >>> My data format is >>> >>> chr coordA coordB value >>> >>> Where approximate distribution of data values are : 5<= value<= 500. >>> Is it possible that your plotting function cannot compute this line >>> because my coordinate intervals are too small? >>> Another possibly relevant issue may be that the coordinate intervals are >>> not fixed length. >>> >>> Any suggestions for course of action would be great. >>> >>> Sincerely, >>> Lionel >> >> ------------------------------ >> >> Message: 4 >> Date: Fri, 01 Apr 2011 10:25:14 -0700 >> From: Galt Barber<[email protected]> >> Subject: Re: [Genome] when is a query excessive. >> To: John Hayward<[email protected]> >> Cc: "[email protected]"<[email protected]> >> Message-ID:<[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> Hi, John! >> >> Queries that take more than a few minutes to run are >> probably inappropriate for the shared public mysql server. >> >> I found this query formulation for you that takes less than one minute: >> >> select name, observed, count(*) from( >> (select name, observed, 'CEU' from hapmapSnpsCEU where chrom = 'Chr16') >> union >> (select name, observed, 'YRI' from hapmapSnpsYRI where chrom = 'Chr16') >> union >> (select name, observed, 'CHB' from hapmapSnpsCHB where chrom = 'Chr16') >> union >> (select name, observed, 'JPT' from hapmapSnpsJPT where chrom = 'Chr16') >> ) resultAlias group by name, observed having count(*) = 4 limit 30; >> >> +-----------+----------+----------+ >> | name | observed | count(*) | >> +-----------+----------+----------+ >> | rs1000014 | A/G | 4 | >> | rs1000047 | C/T | 4 | >> | rs1000077 | C/G | 4 | >> | rs1000078 | A/G | 4 | >> | rs1000100 | A/T | 4 | >> | rs1000174 | A/G | 4 | >> | rs1000178 | C/T | 4 | >> | rs1000192 | A/G | 4 | >> | rs1000193 | A/C | 4 | >> | rs1000454 | C/G | 4 | >> | rs1000455 | A/T | 4 | >> | rs1000710 | G/T | 4 | >> | rs1000711 | C/G | 4 | >> | rs1000720 | A/G | 4 | >> | rs1000742 | C/T | 4 | >> | rs1001157 | A/G | 4 | >> | rs1001170 | G/T | 4 | >> | rs1001171 | A/T | 4 | >> | rs1001302 | A/G | 4 | >> | rs1001362 | C/T | 4 | >> | rs1001366 | C/T | 4 | >> | rs1001493 | C/T | 4 | >> | rs1001554 | A/G | 4 | >> | rs1001608 | C/T | 4 | >> | rs1001631 | C/G | 4 | >> | rs1001655 | A/G | 4 | >> | rs1001722 | G/T | 4 | >> | rs1001776 | C/T | 4 | >> | rs1001861 | A/G | 4 | >> | rs1001871 | C/G | 4 | >> +-----------+----------+----------+ >> 30 rows in set (46.17 sec) >> >> Of course for your own full output, >> you would remove the "limit" clause. >> >> In case you are curious how many there are: >> >> select count(*) from ( >> select name, observed, count(*) from( >> (select name, observed, 'CEU' from hapmapSnpsCEU where chrom = 'Chr16') >> union >> (select name, observed, 'YRI' from hapmapSnpsYRI where chrom = 'Chr16') >> union >> (select name, observed, 'CHB' from hapmapSnpsCHB where chrom = 'Chr16') >> union >> (select name, observed, 'JPT' from hapmapSnpsJPT where chrom = 'Chr16') >> ) resultAlias group by name, observed having count(*) = 4) resultAlias2; >> +----------+ >> | 105841 | >> +----------+ >> 1 row in set (47.60 sec) >> >> >> Another alternative would be to capture the output from each like this: >> >> select name, observed, 'CEU' from hapmapSnpsCEU where chrom = 'Chr16' >> >> for each of your 4 files. >> You could sort them by name (rsId) either with an order by clause in >> sql, or with the unix sort command. >> >> You can even use the unix join command to join them up on the name and >> observed fields. >> >> Once the contents of each of the 4 sets are sorted by name and observed, >> joining them can be very fast. >> >> -Galt >> >> 4/1/2011 8:25 AM, John Hayward: >>> I would like to run queries against the genome-mysql.cse.ucsc.edu >>> database which may be excessive and don't want to cause problems for others. >>> >>> I want to find matches for a particular chromosome which have the same name >>> and observation for tables hapmapSnpsCEU, haphapmapSnpsYRI, mapSnpsCHB, >>> hapmapSnpsJPT. >>> >>> Doing a query to pickup the count of hapmapSnpsCEU for one chromosome took >>> 0.14 seconds. >>> If I do a query to pick up the count joining hapmapSnpsCEU and hapmapSnpCHB >>> took 8.40 seconds. >>> >>> If I join all tables would that constitute an excessive load? >>> >>> Below is the query joining two tables. >>> ====== >>> select count(*) from hapmapSnpsCEU, hapmapSnpsCHB where hapmapSnpsCEU.chrom >>> = 'Chr16' and hapmapSnpsCHB.chrom = 'Chr16' and hapmapSnpsCEU.name = >>> hapmapSnpsCHB.name and hapmapSnpsCEU.observed = hapmapSnpsCHB.observed; >>> ====== >>> johnh... >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> ------------------------------ >> >> Message: 5 >> Date: Fri, 01 Apr 2011 14:16:42 -0400 >> From: "Lionel (Lee) Brooks 3rd"<[email protected]> >> Subject: Re: [Genome] bedgraph data will not display points >> To: Hiram Clawson<[email protected]> >> Cc: [email protected] >> Message-ID:<[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi Hiram, >> >> >From >> http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format >> >> 1. Pseudo /line graphs/ can be drawn with the wiggle tracks by >> setting optional drawing parameters in the display of the track to >> draw /points/ instead of bars with smoothing on to smear the >> points together into a line. >> >> The pseudo line graph functionality is what I desire. >> Previously, it had been possible to do this with bedgraph format files. >> I don't know what "smearing" means. I'm just looking for a quick way to >> draw the moving average as I had been able to do before. >> As I mentioned below, my track line is: >> track type=bedGraph autoScale=on graphType=points windowingFunction=mean >> smoothingWindow=16 >> >> I suppose my solution is to modify my scripts to use the wiggle variable >> step format? >> >> >> thanks, >> -Lionel >> >> >> Hiram Clawson wrote: >>> Good Morning Lionel: >>> >>> The bedGraph drawing mechanism can construct bar graphs at your >>> specified intervals, or when you select graphType=points it will >>> draw only the top of the bar graph at your specified intervals. >>> There is no line drawing except by the trick of "smoothing" points >>> such that they appear to be in a line graph. This only works if >>> the data points are continuous when seen in the genome browser. >>> Smoothing will not smear points into areas where there is no >>> data value specified. >>> >>> The Genome Graphs function of the genome browser: >>> http://genome.ucsc.edu/cgi-bin/hgGenome >>> will only draw lines between your specified points. >>> >>> See also: >>> >>> http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format >>> >>> >>> --Hiram >>> >>> Lionel Brooks wrote: >>>> Hello all, >>>> >>>> I have a bedgraph file. In the past I have used to files to attain >>>> graphic output in the form of a smoothed line but I uploaded my most >>>> recent data set and now I cannot get a line graph. In fact, I'm not >>>> sure what I am looking at because the values that are displayed along >>>> the y-axis are not described with a label. >>>> Here is my track line: >>>> track type=bedGraph autoScale=on graphType=points >>>> windowingFunction=mean smoothingWindow=16 >>>> >>>> My data format is >>>> >>>> chr coordA coordB value >>>> >>>> Where approximate distribution of data values are : 5<= value<= 500. >>>> Is it possible that your plotting function cannot compute this line >>>> because my coordinate intervals are too small? >>>> Another possibly relevant issue may be that the coordinate intervals >>>> are not fixed length. >>>> >>>> Any suggestions for course of action would be great. >>>> >>>> Sincerely, >>>> Lionel >> >> ------------------------------ >> >> Message: 6 >> Date: Fri, 1 Apr 2011 11:18:07 -0700 (PDT) >> From: Hiram Clawson<[email protected]> >> Subject: Re: [Genome] bedgraph data will not display points >> To: "Lionel (Lee) Brooks 3rd"<[email protected]> >> Cc: [email protected] >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=utf-8 >> >> It won't make any difference what type of wiggle format you choose. >> They all draw the same way. >> >> You are going to have to provide me with a URL to your data file >> so I can see what it looks like. >> >> --Hiram >> >> ----- Original Message ----- >> From: "Lionel (Lee) Brooks 3rd"<[email protected]> >> To: "Hiram Clawson"<[email protected]> >> Cc: [email protected] >> Sent: Friday, April 1, 2011 11:16:42 AM >> Subject: Re: [Genome] bedgraph data will not display points >> >> Hi Hiram, >> >> >From >> http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format >> >> 1. Pseudo /line graphs/ can be drawn with the wiggle tracks by >> setting optional drawing parameters in the display of the track to >> draw /points/ instead of bars with smoothing on to smear the >> points together into a line. >> >> The pseudo line graph functionality is what I desire. >> Previously, it had been possible to do this with bedgraph format files. >> I don't know what "smearing" means. I'm just looking for a quick way to >> draw the moving average as I had been able to do before. >> As I mentioned below, my track line is: >> track type=bedGraph autoScale=on graphType=points windowingFunction=mean >> smoothingWindow=16 >> >> I suppose my solution is to modify my scripts to use the wiggle variable >> step format? >> >> >> thanks, >> -Lionel >> >> >> Hiram Clawson wrote: >>> Good Morning Lionel: >>> >>> The bedGraph drawing mechanism can construct bar graphs at your >>> specified intervals, or when you select graphType=points it will >>> draw only the top of the bar graph at your specified intervals. >>> There is no line drawing except by the trick of "smoothing" points >>> such that they appear to be in a line graph. This only works if >>> the data points are continuous when seen in the genome browser. >>> Smoothing will not smear points into areas where there is no >>> data value specified. >>> >>> The Genome Graphs function of the genome browser: >>> http://genome.ucsc.edu/cgi-bin/hgGenome >>> will only draw lines between your specified points. >>> >>> See also: >>> >>> http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format >>> >>> >>> --Hiram >>> >>> Lionel Brooks wrote: >>>> Hello all, >>>> >>>> I have a bedgraph file. In the past I have used to files to attain >>>> graphic output in the form of a smoothed line but I uploaded my most >>>> recent data set and now I cannot get a line graph. In fact, I'm not >>>> sure what I am looking at because the values that are displayed along >>>> the y-axis are not described with a label. >>>> Here is my track line: >>>> track type=bedGraph autoScale=on graphType=points >>>> windowingFunction=mean smoothingWindow=16 >>>> >>>> My data format is >>>> >>>> chr coordA coordB value >>>> >>>> Where approximate distribution of data values are : 5<= value<= 500. >>>> Is it possible that your plotting function cannot compute this line >>>> because my coordinate intervals are too small? >>>> Another possibly relevant issue may be that the coordinate intervals >>>> are not fixed length. >>>> >>>> Any suggestions for course of action would be great. >>>> >>>> Sincerely, >>>> Lionel >> >> ------------------------------ >> >> Message: 7 >> Date: Fri, 1 Apr 2011 14:34:07 -0400 >> From: "Tom Traut"<[email protected]> >> Subject: [Genome] protein families >> To: [email protected] >> Message-ID:<p06240804c9bbcac80186@[152.19.36.114]> >> Content-Type: text/plain; charset=us-ascii; format=flowed >> >> Can I use your site (or any other) to find a listing of major protein >> families? >> >> how many kinases >> how many proteases >> how many G proteins >> >> etc >> -- >> Tom Traut >> >> Professor of Biochemistry& Biophysics >> >> Phone: 919 966-5044 >> FAX: 919 966-2852 >> URL: www.unc.edu/~traut >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> End of Genome Digest, Vol 99, Issue 3 >> ************************************* > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
