Dear list, I am trying to retrieve 5' flanking sequences and 5' utr for several genes. Doing this via biomart.org or, respectively, biomarRt yields different results. An example, I want to retrieve the 5' flanking sequences (3000 bases) plus the 5' utr for the gene with the EntrezID 23704. My R code: library(biomaRt) ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") myseq <- getSequence(id = c(23704), type = "entrezgene", seqType = "coding_gene_flank", upstream = 3154, mart = ensembl) The length of the 5'utr for this gene is exactly is 154, so this query should really yield 3000 upstream bases plus the 5'utr. But, doing this via biomart.org, I get the following: http://www.ensembl.org/Homo_sapiens/Gene/Export?db=core;g=ENSG00000152 049;output=fasta;r=2:223916862-223920353;strand=feature;t=ENST00000281 830;time=1253696359.47541;st=utr5;genomic=5_flanking;_format=HTML The length of both sequences is 3154, but if you blast them, the do not align perfectly. What do I miss? Can it be related to the fact that biomaRt is using the dataset hsapiens_gene_ensembl, version NCBI35 and biomaRt.org is using the Homo Sapiens genes, GRCh37? Thanks a lot, Tefina > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biostrings_2.12.8 IRanges_1.2.3 biomaRt_2.0.0 loaded via a namespace (and not attached): [1] Biobase_2.4.1 RCurl_0.98-1 tools_2.9.1 XML_2.5-3 [[alternative HTML version deleted]]

On Wed, Sep 23, 2009 at 5:22 AM, Tefina Paloma <tefina.paloma@gmail.com>wrote: > Dear list, > > I am trying to retrieve 5' flanking sequences and 5' utr for several genes. > Doing this via biomart.org or, respectively, biomarRt yields different > results. > > An example, I want to retrieve the 5' flanking sequences (3000 bases) plus > the 5' utr for the gene with the EntrezID 23704. > > My R code: > > library(biomaRt) > ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") > myseq <- getSequence(id = c(23704), type = "entrezgene", seqType = > "coding_gene_flank", upstream = 3154, mart = ensembl) > > The length of the 5'utr for this gene is exactly is 154, so this query > should really yield 3000 upstream bases plus the 5'utr. > > But, doing this via biomart.org, I get the following: > > http://www.ensembl.org/Homo_sapiens/Gene/Export?db=core;g=ENSG000001 52049;output=fasta;r=2:223916862-223920353;strand=feature;t=ENST000002 81830;time=1253696359.47541;st=utr5;genomic=5_flanking;_format=HTML > > The length of both sequences is 3154, but if you blast them, the do not > align perfectly. > > Do you mean that they are not the same sequence or that they align to the genome with a gap? This UTR covers two exons, so your sequence should align with a gap. Sean > What do I miss? > Can it be related to the fact that biomaRt is using the dataset > hsapiens_gene_ensembl, version NCBI35 > and biomaRt.org is using the Homo Sapiens genes, GRCh37? > > Thanks a lot, > Tefina > > > > > > > sessionInfo() > R version 2.9.1 (2009-06-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.12.8 IRanges_1.2.3 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.4.1 RCurl_0.98-1 tools_2.9.1 XML_2.5-3 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Tefina Paloma <tefina.paloma at="" ...=""> writes: > Can it be related to the fact that biomaRt is using the dataset > hsapiens_gene_ensembl, version NCBI35 > and biomaRt.org is using the Homo Sapiens genes, GRCh37? > Just a little correction, the dataset hsapiens_gene_ensembl in biomaRt is version NCBI36 (not 35),

Sean Davis <seandavi at="" ...=""> writes: > Do you mean that they are not the same sequence or that they align to the > genome with a gap? This UTR covers two exons, so your sequence should align > with a gap. > > Sean > If I put as query sequence the sequence from biomart.org, and as subject sequence the sequence from biomaRt, the alignment is like below >lcl|2591 Length=3154 Score = 4798 bits (2598), Expect = 0.0 Identities = 2598/2598 (100%), Gaps = 0/2598 (0%) Strand=Plus/Plus Query 534 GCAACCTGAAGCCCTTGGGAGCAACAGCGTACTCCTAACAATGACAACTAAACACAGGCA 593 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1 GCAACCTGAAGCCCTTGGGAGCAACAGCGTACTCCTAACAATGACAACTAAACACAGGCA 60 Query 594 CTGAGCATGTGCATTTGGCCAGACATGGTGCTTTCTTTGCATCATTTCATTGAActattt 653 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 61 CTGAGCATGTGCATTTGGCCAGACATGGTGCTTTCTTTGCATCATTTCATTGAACTATTT 120 Query 654 tattctgttctgttctattctattctattctattctattctattctatttattTAGAGAT 713 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 121 TATTCTGTTCTGTTCTATTCTATTCTATTCTATTCTATTCTATTCTATTTATTTAGAGAT 180 Query 714 CTCGCTCTGTCACCCAGGCTGGAGTGTAGTGGCATGTTCAGACCTCATTGCAGCCTTGAA 773 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 181 CTCGCTCTGTCACCCAGGCTGGAGTGTAGTGGCATGTTCAGACCTCATTGCAGCCTTGAA 240 Query 774 CTCCTGGTCTCGAGTGATCCTCCCACCCCAGCCTCCCAAGTAGCTGGGACTACAGGCACT 833 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 241 CTCCTGGTCTCGAGTGATCCTCCCACCCCAGCCTCCCAAGTAGCTGGGACTACAGGCACT 300 Query 834 CGCCACCAGGCCTAGTTAATTTTTGTAtttttttGTAGAGATGGGGTCTCACTGTGTTGC 893 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 301 CGCCACCAGGCCTAGTTAATTTTTGTATTTTTTTGTAGAGATGGGGTCTCACTGTGTTGC 360 Query 894 CCACGCTGGTCTCAAACACCTGGGTTCAAGTGATTCATCCACCTCAGCCTCTTCAAGCAT 953 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 361 CCACGCTGGTCTCAAACACCTGGGTTCAAGTGATTCATCCACCTCAGCCTCTTCAAGCAT 420 Query 954 TGGGATTACTGAACTAAGACACTGCAGTTGGCCTCGTTTAACTCTAGTAGAAATATCCAT 1013 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 421 TGGGATTACTGAACTAAGACACTGCAGTTGGCCTCGTTTAACTCTAGTAGAAATATCCAT 480 Query 1014 GCAGGAAGTATGTGGGAATCGGGGCAGCAGGGACTCCAAGCAGGCACCCCAGAATTTCTT 1073 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 481 GCAGGAAGTATGTGGGAATCGGGGCAGCAGGGACTCCAAGCAGGCACCCCAGAATTTCTT 540 Query 1074 CTGGGCTGTTCCTTCCCTGACTCCTGCAATTAGTCCTGCTTTTCCTTTGGCTCTGACTTG 1133 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 541 CTGGGCTGTTCCTTCCCTGACTCCTGCAATTAGTCCTGCTTTTCCTTTGGCTCTGACTTG 600 Query 1134 CTTCGTCCTTTGGAATTCATTCTCGATGTTTCCCCACACTCATCTCTTTTCTTGGTTGTA 1193 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 601 CTTCGTCCTTTGGAATTCATTCTCGATGTTTCCCCACACTCATCTCTTTTCTTGGTTGTA 660 Query 1194 TTCCCTTGGGACTGTTGGCTCAGGTTTGGGGATTTATTATGTTTAAAACTTCAGCCTCTG 1253 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 661 TTCCCTTGGGACTGTTGGCTCAGGTTTGGGGATTTATTATGTTTAAAACTTCAGCCTCTG 720 Query 1254 TTTGGCTTCCTGGCACCAGGCTTTGTACTTCCTGCTCCTTGAATCTGGTAACTCCTATCC 1313 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 721 TTTGGCTTCCTGGCACCAGGCTTTGTACTTCCTGCTCCTTGAATCTGGTAACTCCTATCC 780 Query 1314 CCACCTCCTTTCTGCCTACTCAAAGCTTCCAGTCTTTGGTGTTGGACAATCCCTGGATGA 1373 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 781 CCACCTCCTTTCTGCCTACTCAAAGCTTCCAGTCTTTGGTGTTGGACAATCCCTGGATGA 840 Query 1374 TGACCAATCTCGTATGTCCTAAGGTATACAATAAAAAATACCAGGGTCAACAATCAACAG 1433 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 841 TGACCAATCTCGTATGTCCTAAGGTATACAATAAAAAATACCAGGGTCAACAATCAACAG 900 Query 1434 GCATCTCTTTCTTGGGCCCATCTTGTTCTAGTGTCCCAGACATTCCAGTGTAGGCTTAGA 1493 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 901 GCATCTCTTTCTTGGGCCCATCTTGTTCTAGTGTCCCAGACATTCCAGTGTAGGCTTAGA 960 Query 1494 TATAGATGGAAGTGTTCTAGTGTTTATGATGGACACCTGTTGAAAAGACCAAGTCTACCA 1553 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 961 TATAGATGGAAGTGTTCTAGTGTTTATGATGGACACCTGTTGAAAAGACCAAGTCTACCA 1020 Query 1554 TGGCTGAGGTAGCTATGGAGGGTTTTACGTATTAACACAATGGTGAGGGTATCTTTACTG 1613 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1021 TGGCTGAGGTAGCTATGGAGGGTTTTACGTATTAACACAATGGTGAGGGTATCTTTACTG 1080 Query 1614 GTGTGAGCACAGTTCCACTGTATGGATGATCGTGATGCTGGAGTGGTCGATGGTTGGTAC 1673 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1081 GTGTGAGCACAGTTCCACTGTATGGATGATCGTGATGCTGGAGTGGTCGATGGTTGGTAC 1140 Query 1674 CTCCAGTGCCAGCTGGGGATTTATGGATGAACACAGGTGAGTAGTCAAGTGGGAAAAATG 1733 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1141 CTCCAGTGCCAGCTGGGGATTTATGGATGAACACAGGTGAGTAGTCAAGTGGGAAAAATG 1200 Query 1734 GCAGCATTCAGTTCATCTTCCTATTCTTCCTCCAGGTGTCTTCTTAGAATCAGGATCAGG 1793 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1201 GCAGCATTCAGTTCATCTTCCTATTCTTCCTCCAGGTGTCTTCTTAGAATCAGGATCAGG 1260 Query 1794 TGCAAACCCAGGGGGGTTCCTGTAGCAGCAGTGAAAATTCCAGTGCCTAAGCTATATATG 1853 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1261 TGCAAACCCAGGGGGGTTCCTGTAGCAGCAGTGAAAATTCCAGTGCCTAAGCTATATATG 1320 Query 1854 TTCAAGCAGGTCAGGTGGATGTCGCATGCGTCAGTTTGACTACAGCAGAACCATGAGAGA 1913 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1321 TTCAAGCAGGTCAGGTGGATGTCGCATGCGTCAGTTTGACTACAGCAGAACCATGAGAGA 1380 Query 1914 TGTTTCCTTTAGAGTTGGCCCACAAGACAGTCTGGCTGCAATCCACAGGCCACAGACAAC 1973 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1381 TGTTTCCTTTAGAGTTGGCCCACAAGACAGTCTGGCTGCAATCCACAGGCCACAGACAAC 1440 Query 1974 TGGAGGGAGTGGATCTCTCCCAGTTTCCTTCCACTTAGCATGAAAGCCTCAGAATAAGCA 2033 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1441 TGGAGGGAGTGGATCTCTCCCAGTTTCCTTCCACTTAGCATGAAAGCCTCAGAATAAGCA 1500 Query 2034 GCCCAGGGAGCAGAGAGACTGACATTAAAGCCTGCAATTCCTCTTCCAATTTTGATCACA 2093 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1501 GCCCAGGGAGCAGAGAGACTGACATTAAAGCCTGCAATTCCTCTTCCAATTTTGATCACA 1560 Query 2094 GCAGCCATTTAAACACAGGGTCTACCGAGGTTTAAAAAACTTGAACTGTGCTTAGTTGCA 2153 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1561 GCAGCCATTTAAACACAGGGTCTACCGAGGTTTAAAAAACTTGAACTGTGCTTAGTTGCA 1620 Query 2154 CTCTGAAATAGTCCTGCTCCTCCCCTGACCTACGAGAGACAGCAAAGAGACGTGTCAATA 2213 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1621 CTCTGAAATAGTCCTGCTCCTCCCCTGACCTACGAGAGACAGCAAAGAGACGTGTCAATA 1680 Query 2214 GCCTCCGCATGAGGCTTCAGAGGAGCAGCTGTGTATGGCAGGACGGAACAAAACCTGCCC 2273 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1681 GCCTCCGCATGAGGCTTCAGAGGAGCAGCTGTGTATGGCAGGACGGAACAAAACCTGCCC 1740 Query 2274 ATAGTATCTTTTACGACAACATGTTTCCACTTAATGCAGACCACTGAAAAGAATGTGGGA 2333 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1741 ATAGTATCTTTTACGACAACATGTTTCCACTTAATGCAGACCACTGAAAAGAATGTGGGA 1800 Query 2334 GCTTTTaaaaaaaaaTTATTATAAACATAGGTTTGTGACCTTGATGTGGAAGGCAGCTAG 2393 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1801 GCTTTTAAAAAAAAATTATTATAAACATAGGTTTGTGACCTTGATGTGGAAGGCAGCTAG 1860 Query 2394 AATCTCTGCTTTTAGAGGGCTAAGCAACACCAGGCAGCCTTCAATCTTAGAAGGGTTAAG 2453 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1861 AATCTCTGCTTTTAGAGGGCTAAGCAACACCAGGCAGCCTTCAATCTTAGAAGGGTTAAG 1920 Query 2454 CTGAAAGGGTCTCAAAAGGTCACGTGGTTTATATAATCCTACCTGCAGAAGAcccccccc 2513 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1921 CTGAAAGGGTCTCAAAAGGTCACGTGGTTTATATAATCCTACCTGCAGAAGACCCCCCCC 1980 Query 2514 cccGCCAGGCACAACGATTTTACAGACGAGGAATGTGAGGTGCGGAGAGGTTAAGGAAGG 2573 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1981 CCCGCCAGGCACAACGATTTTACAGACGAGGAATGTGAGGTGCGGAGAGGTTAAGGAAGG 2040 Query 2574 ATTTATCTTATTTGCATAAGGAGTGGAAGAACTGAAACCGAAGCCCCAGTTCCTTGACTG 2633 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2041 ATTTATCTTATTTGCATAAGGAGTGGAAGAACTGAAACCGAAGCCCCAGTTCCTTGACTG 2100 Query 2634 TAAATCCCGCACTTGCTTCCAACTGTCTTTCATCCAGATTATGGGATTCAGCTGCCTCTG 2693 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2101 TAAATCCCGCACTTGCTTCCAACTGTCTTTCATCCAGATTATGGGATTCAGCTGCCTCTG 2160 Query 2694 AAAACCTGTAGCCCAATAATGGTTATTCCCCAGGAGCCGCGCGAAGCATGAGCTAATTTT 2753 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2161 AAAACCTGTAGCCCAATAATGGTTATTCCCCAGGAGCCGCGCGAAGCATGAGCTAATTTT 2220 Query 2754 CAGTGAGCGCGGACTTTGGGGTAACGGTTCCAGCACAGCACATCCCTTTCTCCTCTTTTC 2813 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2221 CAGTGAGCGCGGACTTTGGGGTAACGGTTCCAGCACAGCACATCCCTTTCTCCTCTTTTC 2280 Query 2814 ACTCATCGTCACCGCTACCTGAAAACCCTGGCCGGGTGCTGGGGCTTGAGGAGCAGTTCC 2873 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2281 ACTCATCGTCACCGCTACCTGAAAACCCTGGCCGGGTGCTGGGGCTTGAGGAGCAGTTCC 2340 Query 2874 CACTTCCCAGTCTTTTTCACTTTTCACAGCTGCAAAGTTCAGGGAGTTGAACTGCAGTGC 2933 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2341 CACTTCCCAGTCTTTTTCACTTTTCACAGCTGCAAAGTTCAGGGAGTTGAACTGCAGTGC 2400 Query 2934 TTTCAGTTCACTGCTCACTCTGCCACGATCAATCTCTGTTGTAAATTTTCCTCCCAGAGC 2993 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2401 TTTCAGTTCACTGCTCACTCTGCCACGATCAATCTCTGTTGTAAATTTTCCTCCCAGAGC 2460 Query 2994 ACGTGACGATGCACTTCTTGACTATATATCCCAACTGCAGCAGCGGAGTTGTCAGAGCGC 3053 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2461 ACGTGACGATGCACTTCTTGACTATATATCCCAACTGCAGCAGCGGAGTTGTCAGAGCGC 2520 Query 3054 AGAGCCGGACAGAGCAGAAGAACCCTCTTGGACTGGACGATTTGGGAATTCAAAACTTGG 3113 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2521 AGAGCCGGACAGAGCAGAAGAACCCTCTTGGACTGGACGATTTGGGAATTCAAAACTTGG 2580 Query 3114 GACAAACTGTCAGCCTTG 3131 |||||||||||||||||| Sbjct 2581 GACAAACTGTCAGCCTTG 2598

Sean Davis <seandavi at="" ...=""> writes: > Do you mean that they are not the same sequence or that they align to the > genome with a gap? This UTR covers two exons, so your sequence should align > with a gap. > > Sean > As far as I understand, the sequences should align to each other perfectly. Is this right? Best, Tefina