On a related but more primitive topic, anyone have test cases or new tools for CRISPR's? ( these come up on pubmed, but I'll pass thislink along for background since it is all I have in front of me now:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17537822 ) I could run my modified tools to find suspects on the e coli strains I happen to have, $ date;$progpath/rules_annotater -fastas f2 -rci -regex "[\-1]{24,47}.{26,72}[\-1]{24,47}"> f2_crisps 2>f2_diags ;date Wed Feb 20 14:04:42 EST 2008 Wed Feb 20 14:04:53 EST 2008 and in fact determine that there were some suspects regularly separated by about 120 bases, but have no idea if these are "right:" >gi|48994873|gb|U00096.2| Escherichia coli K12 MG1655, complete genome $ cat f2_crsips | awk '{print $1" "$1-last" "$3; last=$1}' [...] 2660373 94198 CACTGTAGGCCTGATAAGACGCATTACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCAT 2660488 115 TACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCATTACGCGTCGCATCAGGCAACGGCT 2875903 215415 CCCGGTTTATCCCCGCTGGCGCGGGGAACTCCCGGGGGATAATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGG 2876027 124 CGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTCCGGTTTATCCCCGCTGGCGCGGGG 2876149 122 CGGTTTATCCCCGCTGGCGCGGGGAACTCGCAGGCGGCGACGCGCAGGGTATGCGCGATTCGCGGTTTATCCCCGCTGGCGCGGGG 2876273 124 CGGTTTATCCCCGCTGGCGCGGGGAACTCTCAACATTATCAATTACAACCGACAGGGAGCCCGGTTTATCCCCGCTGGCGCGGGG 2876394 121 GCGGTTTATCCCCGCTGGCGCGGGGAACTCTGCGTGAGCGTATCGCCGCGCGTCTGCGAAAGCGGTTTATCCCCGCTGGCGCGGG 2902035 25641 GGTTTATCCCCGCTGGCGCGGGGAACTCGACAGAACGGCCTCAGTAGTCTCGTCAGGCTCCGGTTTATCCCCGCTGGCGCGGGGA 2902155 120 TCGGTTTATCCCCGCTGGCGCGGGGAACACGGGCGCACGGAATACAAAGCCGTGTATCTGCTCGGTTTATCCCCGCTGGCGCGGG 2902279 124 GGTTTATCCCCGCTGGCGCGGGGAACACGAAATGCTGGTGAGCGTTAATGCCGCAAACACAGGTTTATCCCCGCTGGCGCGGGGA 2945406 43127 GACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCA 2945554 148 TAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATCAAATTTGATGAAGTAAAAGCAGTACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAA 3229358 283804 CTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCG [...] Wasn't sure if anyone knows about these things- known test cases or open issues. Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only [EMAIL PROTECTED] Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on [EMAIL PROTECTED] if no reply here. Thanks. > Date: Fri, 22 Feb 2008 15:23:17 +0800 > From: [EMAIL PROTECTED] > To: [email protected] > Subject: Re: [BiO BB] LINES SINES MICROSATELLITES and TFOs > > better use WU-BLAST as enginee. > > On 1/12/08, ocean wrote: >> >> >> i think you can try ucsc, use the repeatmasker information of human >> >> the following is RepeatMasker (rmsk) Track Description >> >> Short interspersed nuclear elements (SINE), which include ALUs >> Long interspersed nuclear elements (LINE) >> Long terminal repeat elements (LTR), which include retroposons >> DNA repeat elements (DNA) >> Simple repeats (micro-satellites) >> Low complexity repeats >> Satellite repeats >> RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA) >> Other repeats, which includes class RC (Rolling Circle) >> Unknown >> >> >> >> 在2008-01-10，"Narendran GR" 写道： >> >> Hi friends.... >> >>> I want to collect information on LINES SINES MICROSATELLITES and TFOs in >>> Human genome... >>> >>> Where can i find the information??? >>> Is there any information about them in NCBI??? >> >> Please help me with the same.... >>> >> >> -- >> Regards >> Narendran G R >> _______________________________________________ >> BBB mailing list >> [email protected] >> http://www.bioinformatics.org/mailman/listinfo/bbb >> _______________________________________________ >> BBB mailing list >> [email protected] >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > Best Regards > Sheng Wang > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Connect and share in new ways with Windows Live. http://www.windowslive.com/share.html?ocid=TXT_TAGHM_Wave2_sharelife_012008 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
