Virtual Diegest (ISPaR)
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T-RFLP Analysis (APLAUS+)
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T-RFLP Analysis (PAT+)
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P.S.P.A.
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E.R.P.A.
November 21, 2008
MiCA: Virtual Digest (ISPaR)
Do you know ...
MiCA website was developed by students and faculty of the Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. This research was funded by the P&G company.
P&G
IBEST
Program of BCB
Biological Sciences
University of Idaho
Forward Primer:
Select a forward primer here ...
Arc-109f ACKGCTCAGTAACACGT
Arc-112f GCTCAGTAACACGTGG
CYA106f CGGACGGGTGAGTAACGCGTGA
CYA359f GGGGAATYTTCCGCAATGGG
CYA432f CCGCGTGAGGGAGGAAGG
Eub-1055f ATGGCTGTCGTCAGCT
Eub-341f CCTACGGGAGGCAGCAG
Eub-8f AGAGTTTGATCCTGGCTCAG
Eub-8fm AGAGTTTGATCMTGGCTCAG
Eub-968f AACGCGAAGAACCTTAC
Uni-519f CAGCAGCCGCGGTAATAC
Uni-519fm CAGCMGCCGCGGTAATWC
or enter here:
Reverse Primer:
Select a reverse primer here ...
1062r ACAGCCATGCAGCACCT
1387r CCCGGGAACGTATTCACCGC
1492r GYTACCTTGTTACGACTT
Arc-533r TTACCGCGGCGGCTGGCA
Arc-934r GTGCTCCCCCGCCAATTCCT
CYA781r(a) GACTACTGGGGTATCTAATCCCATT
CYA781r(b) GACTACAGGGGTATCTAATCCCTTT
CYA792r TCCCCTAGCTTTCGTCCC
Eub-1113r GGGTTGCGCTCGTTG
Eub-1401r CGGTGTGTACAAGGCCCGGGAACG
Eub-536r GWATTACCGCGGCKGCTG
Eub-539r ATCGTATTACCGCGGCTGCTGGCA
Eub-926r CCGTCAATTCCTTTRAGTTT
Uni-1406r ACGGGCGGTGTGTRC
Uni-1513r GGGTACCTTGTTACG
or enter here:
Restriction Enzyme:
Select a restriction enzyme here ...
Acc II CG^CG
Afa I GT^AC
Alu I AG^CT
BAM HI G^GATCC
Bfa I C^TAG
Bsh1236 I CG^CG
Bsp106 I ^GATC
BstU I CG^CG
BsuR I GG^CC
Cfo I GCG^C
CviR I TG^CA
DdeI C^TNAG
Dpn I (methA) GA^TC
Dpn II ^GATC
Eco RI G^AATTC
FnuD II CG^CG
Hae III GG^CC
Hap II C^CGG
Hha I GCG^C
HinP1 I G^CGC
HinfI G^ANTC
Hpa II C^CGG
Hpy 1881 TCN^GA
Hpy 188III TC^NNGA
HpyCH4 IV A^CGT
HpyCH4 V TG^CA
Hsp92 II CATG^
Mae I C^TAG
Mae II A^CGT
Mbo I ^GATC
Mse I T^TAA
Msp I C^CGG
Mvn I CG^CG
Nde II ^GATC
Nla III CATG^
Pal I GG^CC
Rsa I GT^AC
Sau3A I ^GATC
Sau96I G^GNCC
ScrFI CC^NGG
Stu I AGG^CCT
Taq I T^CGA
Tha I CG^CG
Tru9 I T^TAA
Tsp509 I ^AATT
TthHB8 I T^CGA
or enter here:
Restriction Enzyme:
Select a restriction enzyme here ...
Acc II CG^CG
Afa I GT^AC
Alu I AG^CT
BAM HI G^GATCC
Bfa I C^TAG
Bsh1236 I CG^CG
Bsp106 I ^GATC
BstU I CG^CG
BsuR I GG^CC
Cfo I GCG^C
CviR I TG^CA
DdeI C^TNAG
Dpn I (methA) GA^TC
Dpn II ^GATC
Eco RI G^AATTC
FnuD II CG^CG
Hae III GG^CC
Hap II C^CGG
Hha I GCG^C
HinP1 I G^CGC
HinfI G^ANTC
Hpa II C^CGG
Hpy 1881 TCN^GA
Hpy 188III TC^NNGA
HpyCH4 IV A^CGT
HpyCH4 V TG^CA
Hsp92 II CATG^
Mae I C^TAG
Mae II A^CGT
Mbo I ^GATC
Mse I T^TAA
Msp I C^CGG
Mvn I CG^CG
Nde II ^GATC
Nla III CATG^
Pal I GG^CC
Rsa I GT^AC
Sau3A I ^GATC
Sau96I G^GNCC
ScrFI CC^NGG
Stu I AGG^CCT
Taq I T^CGA
Tha I CG^CG
Tru9 I T^TAA
Tsp509 I ^AATT
TthHB8 I T^CGA
or enter here:
Restriction Enzyme:
Select a restriction enzyme here ...
Acc II CG^CG
Afa I GT^AC
Alu I AG^CT
BAM HI G^GATCC
Bfa I C^TAG
Bsh1236 I CG^CG
Bsp106 I ^GATC
BstU I CG^CG
BsuR I GG^CC
Cfo I GCG^C
CviR I TG^CA
DdeI C^TNAG
Dpn I (methA) GA^TC
Dpn II ^GATC
Eco RI G^AATTC
FnuD II CG^CG
Hae III GG^CC
Hap II C^CGG
Hha I GCG^C
HinP1 I G^CGC
HinfI G^ANTC
Hpa II C^CGG
Hpy 1881 TCN^GA
Hpy 188III TC^NNGA
HpyCH4 IV A^CGT
HpyCH4 V TG^CA
Hsp92 II CATG^
Mae I C^TAG
Mae II A^CGT
Mbo I ^GATC
Mse I T^TAA
Msp I C^CGG
Mvn I CG^CG
Nde II ^GATC
Nla III CATG^
Pal I GG^CC
Rsa I GT^AC
Sau3A I ^GATC
Sau96I G^GNCC
ScrFI CC^NGG
Stu I AGG^CCT
Taq I T^CGA
Tha I CG^CG
Tru9 I T^TAA
Tsp509 I ^AATT
TthHB8 I T^CGA
or enter here:
Select Database:
RDP Release 9.60, 160,583 Good Quality (>1200) 16S rRNA
RDP Release 9.60, 511,847 Bacterial SSU 16S rRNA
NCBI Archaeon 16S rRNA Gene Sequences
16S Bacterial rRNA Sequences (by A. Hartman)
Methyl Coenzyme-M Reductase (mcrA) (by G.M. Nava)
Dissimilatory Sulfite Reductase A, B (by G.M. Nava)
Nitrous Oxide Reductase (nosZ) Gene Sequences
H.Q. 16S Gut Organisms (provided by S. Bhandari)
Pig Bacterial 16S rRNA (provided by Hojberg et al.)
Dr. Fouke's 16S Sequences (provided by Maalouf et al.)
Greengenes 16S rDNA data (http://greengenes.lbl.gov)
Sequences provided by Allison E. Murray (NR99_778)
Sequences provided by Michael Falk of U.C. Davis
18S sequences from yeasts provided by A. Marcobal
Sensitivity:
digest allows at most
0
1
2
3
4
5
6
7
8
9
10
mismatches within
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
bases from 5' end of primer
Report:
Only the shortest ones
All fragment lengths
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Forward fragments
Reverse fragments
Organism names
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Last updated on September 23 2005 13:05:38.