[BiO BB] LINES SINES MICROSATELLITES and TFOs

[Mike Marchywka]

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
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> Date: Fri, 22 Feb 2008 15:23:17 +0800
> From: bsmagic at gmail.com
> To: bbb at bioinformatics.org
> 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
>> BBB at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bbb
>> _______________________________________________
>> BBB mailing list
>> BBB at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bbb
>>
>
>
>
> --
> Best Regards
> Sheng Wang
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb

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