Example of Pair Correlation Analysis

CRASP
Correlation analysis of
protein sequences

ANALYSIS OF PAIR POSITIONAL CORRELATIONS
(advanced setup example)

Sequence alignment data:
Load from screen:

>AP1_CHICK
SQERIKAERKRMRNRIAASKCRKRKLERIAR
>AP1_DROME
AQEKIKLERKRQRNRVAASKCRKRKLERISK
>AP1_KLULA
PLETEAKDKRTAQNRAAQRAFRERRERKMKE
>AP1_SCHPO
NSDQEPSSKRKAQNRAAQRAFRKRKEDHLKA
>ATF1_HUMAN
DDPQLKREIRLMKNREAARECRRKKKEYVKC
>ATF1_SCHPO
ETDEEKRKSFLERNRQAALKCRQRKKQWLSN
>ATF2_MOUSE
EDPDEKRRKFLERNRAAASRCRQKRKVWVQS
>ATF3_HUMAN
PEEDERKKRRRERNKIAAAKCRNKKKEKTEC
>ATF3_MOUSE
PEEDERKRRRRERNKIAAAKCRNKKKEKTEC
>ATF4_HUMAN
GEKLDKKLKKMEQNKTAATRYRQKKRAEQEA
>ATF4_MOUSE
TEKLDKKLKKMEQNKTAATRYRQKKRAEQEA
>BBF2_DROME
EEKSLKKIRRKIKNKISAQESRRKKKEYMDQ
>CAD1_YEAST
RIDSEAKSRRTAQNRAAQRAFRDRKEAKMKS
>CNC_DROME
QLSLIRDIRRRGKNKVAAQNCRKRKLDQILT 
>CPC1_NEUCR
EDPSDVVAMKRARNTLAARKSRERKAQRLEE
>CREA_HUMAN
EEATRKRELRLMKNREAAKECRRRKKEYVKC
>CREA_MOUSE
EEATRKRELRLMKNREAARECRRKKKEYVKC
>CREB_BOVIN
EEAARKREVRLMKNREAARECRRKKKEYVKC
>CREB_CHLVR
EEATRKRELRLYKNREAARECRRKKKEYVKC
>FOSB_HUMAN
PEEEEKRRVRRERNKLAAAKCRNRRRELTDR
>FOSX_MSVFR
PEEEVKRRIRRERNKMAAAKCRNRRRELTDT
>FOS_AVINK
PEEEEKRRIRRERNKMAAAKCRNRRRELTDT
>FOS_CYPCA
PEEEEKKRVRRERNKMAAAKCRNRRRELTDT
>FOS_FUGRU
PEEEEKKRIRRERNKQAAAKCRNRRRELTDT
>FRA1_HUMAN
PEEEERRRVRRERNKLAAAKCRNRRKELTDF
>FRA2_CHICK
PEEEEKRRIRRERNKLAAAKCRNRRRELTEK
>FRA_DROME
PEEEQKRAVRRERNKQAAARCRKRRVDQTNE
>GCN4_YEAST
PESSDPAALKRARNTEAARRSRARKLQRMKQ
>JUNB_CYPCA
NQERIKAERKRLRNRLAATKCRKRKLERISR
>JUNB_HUMAN
DQERIKVERKRLRNRLAATKCRKRKLERIAR
>JUND_CHICK
TQERIKAERKRLRNRIAASKCRKRKLERISR
>MAFF_CHICK
EVARLKQRRRTLKNRGYAASCRVKRVCQKEE
>MAFG_CHICK
EIIQLKQRRRTLKNRGYAASCRVKRVTQKEE
>MAFK_CHICK
EVIRLKQRRRTLKNRGYAASCRIKRVTQKEE
>MAFK_MOUSE
EVTRLKQRRRTLKNRGYAASCRIKRVTQKEE
>NRL_HUMAN
EALRLKQRRRTLKNRGYAQACRSKRLQQRRG
>PCR1_SCHPO
EVDDEKRRRILERNRIAASKFRQKKKEWIKE
>PDR4_YEAST
DLDPETKQKRTAQNRAAQRAFRERKERKMKE
>SKO1_YEAST
EEQERKRKEFLERNRVAASKFRKRKKEYIKK
>TJUN_AVIS1
SQERIKAERKRMRNRIAASKSRKRKLERIAR
>TMAF_AVIS4
EVIRLKQKRRTLKNRGYAQSCRFKRVQQRHV
>XBP1_HUMAN
LSPEEKALRRKLKNRVAAQTARDRKKARMSE

Load from file:
Format

Calculation parameters setup:

Amino Acid Quantity:

Type of matrix:

Variability threshold:

Gap number threshold:

(%)

Selected sequence #

First AA number

Position indexing type

Weights setup:

Tree in (*.ph) format or User Weights:
Load from screen:
( ( ( ( ( ( ( AP1_CHICK:0.00634, TJUN_AVIS1:0.02592) :0.04843, JUND_CHICK:0.04835) :0.02110, ( JUNB_CYPCA:0.04460, JUNB_HUMAN:0.05218) :0.02728) :0.03775, AP1_DROME:0.11548) :0.14950, CNC_DROME:0.30211) :0.04789, ( ( ( ATF1_SCHPO:0.21749, ( ATF2_MOUSE:0.22263, PCR1_SCHPO:0.16447) :0.02445) :0.01627, SKO1_YEAST:0.20954) :0.08574, ( ( ATF3_HUMAN:0.02078, ATF3_MOUSE:0.01148) :0.18505, ( ( ( FOSB_HUMAN:0.04222, FRA1_HUMAN:0.05455) :0.02119, ( ( ( FOSX_MSVFR:0.02500, FOS_AVINK:0.00726) :0.02492, ( FOS_CYPCA:0.03258, FOS_FUGRU:0.03194) :0.00734) :0.03008, FRA2_CHICK:0.05863) :0.00301) :0.09392, FRA_DROME:0.18430) :0.05588) :0.08827) :0.01259) :0.00765, ( ( ( ( ( AP1_KLULA:0.09041, PDR4_YEAST:0.10314) :0.05835, CAD1_YEAST:0.15133) :0.04349, AP1_SCHPO:0.20651) :0.17144, XBP1_HUMAN:0.29227) :0.02330, ( ( ( ATF1_HUMAN:0.12446, ( CREA_HUMAN:0.04858, ( ( CREA_MOUSE:0.01369, CREB_CHLVR:0.01857) :0.02558, CREB_BOVIN:0.03894) :0.01593) :0.05296) :0.14849, BBF2_DROME:0.27691) :0.02881, ( ( ( MAFF_CHICK:0.04708, ( MAFK_CHICK:0.01530, MAFK_MOUSE:0.01696) :0.03357) :0.00885, MAFG_CHICK:0.06373) :0.08555, ( NRL_HUMAN:0.12264, TMAF_AVIS4:0.13543) :0.02937) :0.21917) :0.03573) :0.01194, ( ( ATF4_HUMAN:0.01653, ATF4_MOUSE:0.01573) :0.35620, ( CPC1_NEUCR:0.21256, GCN4_YEAST:0.20680) :0.14380) :0.02218);
Load from file:

Output parameters setup:

Significance level:

(%)

Optional parameters setup

Clustering highly correlated positions:

Show rearranged matrix:

Clustering cutoff value:

Detecting regions of high density of significant correlation:

Correlation threshold:

Correlation sign:

Significance level:

(%)