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CBCDetect

Figure 4.2: CBCDetect calculates compensatory base changes in all against all of the aligned sequences. If a multiple alignment is used, the output is a count matrix (uncorrected p-distances), that now can be used as input for PHYLIP, or BIONJ.

The input of CBCDetect is a part of the output from RNAforester or a part of the output from MARNA to be put in by copy & paste:

From RNAforester you get (only pairwise alignments) in the following format:

> Name1
and  
> Name2

global alignment score:17
((((...))))
((((...))))
augcuuugcau
augggggccau
From MARNA you get (pairwise or multiple alignments) in the following format:

AB013372         GCGCCCG-UAGCUCA-A-----UU--GG-------A-UAGAGCG---UUUGA-C-UACGGAUCAAAAGGUUAGGGGUUCGA---CUCCUCUCGGGCGCG
AB013373         GCGGAAG-UAGUUCA-G------U--GG-------U--AGAACA---CCACCUU-GCCAA-GGUGGGGGUCGCGGGUUCGAA-UCCCGU--CUUCCGCU
AE000930         -GGCCCG-UAGCUCAGA-----CU--GG-------G--AGAGCG---CCGCCCUUGC-A-AGGCGGAGGCCCCGGGUUCAAA-UCCCGG-U-GGGUCCA
AB067577         GGGCUAU-UAGCUCA-G-----GU--GG-------U-UAGAGCG---CACCCCU-GAUAA-GGGUGAGGUCCCUGGUUC-AAGUCCAGG--AUGGCCCA
AF034440         GUUGAUG-UAGCUUA-A-----CC--C-----------AAAGCA---AGGCACU-GAAAA-UGCCUAGAU-GAGU-CUCCCA---ACUC--CAUAAACA
AL590385         GU-CAGGAU-GGCCG-AGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCC---CU---GGAGG----CGUGGGUUCGAA-UCCCAC-UCCUG-ACA
Seq              gNgcaNg_UaGcuca_a_____cu__gg_______u_NAgagCg___ccNcccu_gaNaa_ggNggaggucgcggguUCgaa_ucccgN_ucNggcNCa


AB013372         (((((((-..((((.-.-----..--..-------.-..)))).---(((((-(-....).))))).....(((((.....---)))))..))))))).
AB013373         (((((((-..((((.-.------.--..-------.--.)))).---((((((.-....)-))))).....(((((......-.)))))--))))))).
AE000930         -(((((.-..((((...-----..--..-------.--.)))).---(((((.....-.-.))))).....(((((......-.)))))-.-)))))..
AB067577         ((((((.-..((((.-.-----..--..-------.-..)))).---(((((..-.....-))))).....(((((...-....)))))--.)))))).
AF034440         (((.(((-..((((.-.-----..--.-----------.)))).---(((((.(-....)-)))))....-((((-......---))))--))).))).
AL590385         ((-(((((.-((((.-.(((((.......))))).....))))...((((((.---..---)))))----)(((((......-.)))))-)))))-)).
Str(50%)         (((((((_..((((._._____..__.._______._..)))).___(((((.._....._))))).....(((((......_.)))))_.))))))).
Str(60%)         ((((((._..((((._._____..__.._______._..)))).___(((((.._....._))))).....(((((......_.)))))_..)))))).
Str(70%)         ((((((._..((((._._____..__.._______._..)))).___(((((.._....._))))).....(((((......_.)))))_..)))))).
Str(80%)         ((((((._..((((._._____..__.._______._..)))).___(((((.._....._))))).....(((((......_.)))))_..)))))).
Str(90%)         .(..((._..((((._._____..__.._______._..)))).___(((((.._....._))))).....((((......._..))))_..))..)..
or you can use the following more easier format:
Name1 AUGCUUUGCAU
Name2 AUGGGGGCCAU
Name3 AAAAUUUUUUU
          
Name1 ((((...))))
Name2 ((((...))))
Name3 ((((...))))
Note: use CBCDetect only with RNA data NOT with DNA.

The output of CBCDetect is a count- (resp. a distance) matrix (uncorrected p-distances)of CBCs, which could be used as input for cbcTree.