|
Документ взят из кэша поисковой машины. Адрес
оригинального документа
: http://www.genebee.msu.ru/services/alicomp/help.html
Дата изменения: Sun Aug 26 20:31:08 2001 Дата индексирования: Tue Oct 2 01:40:29 2012 Кодировка: |
1 - max - offset color range is 1 to maximum value; min - max - offset color range is minimum to maximum value.The second option works only when both smallest left offset and smallest right offset are greater than 1.
Offset comparison - two basic comparison pictures. First one contains
offsets of the first alignment relative to the second
alignment. Second picture contains offsets of the second
alignment relative to the first alignment.
Column values comparison - two pictures (the 1st alignment versus the 2nd
one, and 2nd versus 1st) with comparison of column
values in the range best to worst. X axe contains percent
of columns of alignment. These pictures are useful to
compare alignments with very different lengths too.
Col. values comparison 2 - two pictures (the 1st alignment versus the 2nd
one, and 2nd versus 1st) with comparison of column
values in the range best to worst. X axe contains quantity
of columns of the 1st or 2nd alignment respectively.
Even - all column space are colored;
Sparse - every column is colored with respect to the column weight:
less weight more space is left uncolored;
Very sparse - more space is left uncolored. So, important columns
(with greater weight) are better seen.
All groups - all letter groups are colored;
Max group at column - colored only letters of a maximum (dominant) group
at every column;
Column values - a few statistical functions (column values):
- the number of letters in max group at the column,
- the number of same letters at the column,
- the number of groups at the column,
- the weight of the column;
Column values (best-to-worst) - same functions but another ordering.
That is in the range best to worst over X-axe.
Also you can get a picture when only selected groups are colored.
AUTO - the program defines the molecular type of the source
alignment and selects respective group type;
Protein - protein groups will be used (see below);
Nucleotide - nucleotide groups will be used (see below);
You can select the color group type, protein or nucleotide, or leave it to
the program (the type "AUTO") to decide which one should be used.
There are the following protein letter groups:
1. _______A G _______________
2. _______C _________________
3. _______D E N Q B Z _______
4. _______I L M V ___________
5. _______F W Y _____________
6. _______H _________________
7. _______K R _______________
8. _______P _________________
9. _______S T _______________
10. _______Others ____________
There are the following nucleotide letter groups:
1. _______A _________________
4. _______C _________________
6. _______G _________________
4. _______T U _______________
5. _______Others ____________
Example of two alignments to be compared:
First alignment:
.**.. ....+. .....+.. +.......++.. . +.... +.... ....*. ..
HCVPCP2 ( 1) EDGVNVHDVTVTTDKSFEQQV-GVIADKDKDLSGAVPSDLNTSELLTK-----AIDV-DW
TGVPCP2 ( 1) EDNVNHERVSVSFDKTYGEQLKGTVVIKDKDVTNQLPSAFDVGQKVIK-----AIDI-DW
MHVPCP2 ( 1) VDGVNFRSCCVAEGEVFGKTL-GSVFCDGINVTKVRCSAIYKGKVFFQysdLSEADLvAV
MHVPCP1 ( 1) REGIAEAKATVCAD--AVDACPDQVEA--FEIEKVEDSILDELQTELN----APADK-TY
HCVPCP1 ( 1) EEGGNDLSLPVMISEWPLSVQQAQQEATLPDIAEDVVDQVEEVNSIFD---IETVDV---
TGVPCP1 ( 1) SEG--------------AEGTSSQEEVETVEVADITSTD-EDVD-IVE---VSAKDD-PW
IBVPCP ( 1) EDGVKYRSIVLKPGDSLGQ--FGQVYAKNK-IV-FTADDVEDKEILYV----PTTDK-SI
....+..+...+..... ....++... .+....+..++***+++.++.+* ....+.
HCVPCP2 ( 54) VEFYGFKDAVTFATVDHSAF-AYESAV-VNGIRVLKTSDNNCWVNAVCIALQYSKPHFIS
TGVPCP2 ( 55) QAHYGFRDAAAFSASSHDAY-KFEVVT-HSNFIVHKQTDNNCWINAICLALQRLKPQWKF
MHVPCP2 ( 60) KDAFGFDEPQLLKYYTMLGMCKWPVVV-CGNYFAFKQSNNNCYINVACLMLQHLSLKFPK
MHVPCP1 ( 52) EDVLAFDAVCSEALSAFYAVPSDETHFkVCGFYSPAIERTNCWLRSTLIVMQSLPLEFKD
HCVPCP1 ( 55) -----KHDVSPF-------EMPFEELN---GLKILKQLDNNCWVNSVMLQIQLTGI----
TGVPCP1 ( 41) AAAVDVQEAEQF----NPSLPPFKTTN-LNGKIILKQGDNNCWINACCYQLQ----AFDF
IBVPCP ( 52) LEYYGL-DAQKYVIYLQTLAQKWNVQY-RDNFLILEWRDGNCWISSAIVLLQAAKIRFKG
....+*..*. *... **..++.......+. .*.. .+ .+. ....*.. . . . .
HCVPCP2 ( 112) QGLDAAWNKFVLGDVEIFVAFVYYVARLMKGDKGDAEDTLTKLSKYLANEAQV-QLEHYS
TGVPCP2 ( 113) PGVRGLWNEFLERKTQGFVHMLYHISGVKKGEPGDAELMLHKLGDLMDNDCEI-IVTHTT
MHVPCP2 ( 119) WQWQEAWNEFRSGKPLRFVSLVLAKGSFKFNEPSDSIDFMR--VVLREADLSGATCNLEF
MHVPCP1 ( 112) LEMQKLWLSYKAGYDQCFVDKL--VKSVPKSIILPQGGYVADFAYFFLSQCSF-KAYANW
HCVPCP1 ( 96) LDGDYAMQFFKMGRVAKMIERCYTAEQCIRGAMGDVGLCMYRL----LKDLHTGFMVMDY
TGVPCP1 ( 92) FN-NEAWEKFKKGDVMDFVNLCYAATTLARGHSGDAE-YLLEL---MLNDYSTAKIVLAA
IBVPCP ( 110) F-LTEAWAKLLGGDPTDFVAWCYASCTAKVGDFSDANWLLANLAEHFDADYTNAFLKKRV
.* .*... .. .++. ..+..... ........* .+.. ......+......+..
HCVPCP2 ( 171) SCVECDAKFK--NSVASINSAIVCASVKRDGVQVGYCVHGIK--YYSRVRSVRGRAIIVS
TGVPCP2 ( 172) ACDKC-------AKVEKFVGPVVAAPLAIHGTD-ETCVHGVS-VNV-KVTQIKGTVAITS
MHVPCP2 ( 177) VC-KCGVKQEQRKGVDA---VMHFGTLDKGDLVRGYNIACTCgSKLVHCTQFNVPFLICS
MHVPCP1 ( 169) RCLECDMELK-LQGLDA---MFFYGDVVSHMCK---CGNSMT------LLSADIPYTLHF
HCVPCP1 ( 152) KC-SC-----TSGRLEE-SGAVLFCTPTKKAFPYGTCLNCNA-PRMCTIRQLQGTIIFVQ
TGVPCP1 ( 147) KC-GCGEK---EIVLER---AVFKLTPLKESFNYGVCGDCMQ-VNTCRFLSVEGSGVFVH
IBVPCP ( 169) SC-NCGIKSYELRGLEACIQPVRATNLLHFKTQYSNCPTCGA-NNTDEVIEASLPYLLLF
. . . ....+....+.*....**+.. . .... ..*+ ..... . . ....
HCVPCP2 ( 227) VEQ-LEPCAQSRLLSGVAYTAFSGPVDKGHYTVYDTAKKS-MYDG---DRFV--KHD-LS
TGVPCP2 ( 222) LIG----PIIGEVLEATGYICYSGSNRNGHYTYYDNRNGL-VVDAEKAYHFNRDLLQVTT
MHVPCP2 ( 233) NTP--EGRKLPDDV--VAANIFTGG-SVGHYTHVKCKPKYqLYDACNVNKVSEAKGNFTD
MHVPCP1 ( 216) GVR-DDKFCAFYTPRKVFRAACAVDVNDCHSMAVVEGKQI---DGKVVTKFIGDKFDFMV
HCVPCP1 ( 204) QKP-EPVNPVSFVVKPVCSSIFRGAVSCGHYQTNIYSQNL-CVDGFGVNKIQPWTNDALN
TGVPCP1 ( 199) DILsKQTPEAMFVVKPVMHAVYTGTTQNGHYMVDDIEHGY-CVDGMGIKPLKK--RCYTS
IBVPCP ( 227) ATD--GPATVDCDEDAVGTVVFVGSTNSGHCYTQAAGQAF---DNLAKDRKFGKKSPYIT
.+....... ...... .. ..+... ++ ...
HCVPCP2 ( 279) LLSVTSVVM------VGGYVAPVNTVKPKPVINQ
TGVPCP2 ( 277) AIASNFVVKK-PQAEERPKNCAFNKVAASPKIVQ
MHVPCP2 ( 288) CLYLKNLKQTFSSVLTTFYLDDVKCVEYKPDLSQ
MHVPCP1 ( 272) GYGMTFSMSPFELAQLYGSCITPNVCFVK-----
HCVPCP1 ( 262) TICIKDADY---NAKVEISVTPIKN---------
TGVPCP1 ( 256) TLFINANVM--TRAEKPKQEFKVEKVEQQPIVEE
IBVPCP ( 282) AMYTRFAFK----NETSLPVAKQSKGKSKS-VKE
Second alignment:
HCVPCP2 EDGVNVHDVTVTTDKSF-EQQVGVIADKDKDLSGAVPSDLNTSELLTKAIDVDWVEFYGF
TGVPCP2 EDNVNHERVSVSFDKTYGEQLKGTVVIKDKDVTNQLPSAFDVGQKVIKAIDIDWQAHYGF
MHVPCP2 VDGVNFRSCCVAEGEVF-GKTLGSVFCDGINVTKVRCSAIYKGKVFFQYSDLSEADLVAV
TGVPCP1 --------SEGAEGTSS-QEEVETVEVADITST-----DEDVDIVEVSAKDDPWAAAVDV
HCVPCP1 -----------EEGGND--LSLPVMISEWPLSVQQAQQEATLPDIAEDVVDQVEEVNSIF
IBVPCP EDGVKYRSIVLKPGDSL--GQFGQVYAKNKIVFTAD-DVEDKEILYVPTTDKSILEYYGL
MHVPCP1 REGIAEAKATVCADAVD--ACPDQVEAFEIEKVEDSILDELQTELNAPA-DKTYEDVLAF
HCVPCP2 KDAVTFATVDHSAF-------AYESAVVNGIRVLKTSDNNCWVNAVCIALQYSKPHFISQ
TGVPCP2 RDAAAFSASSHDAY-------KFEVVTHSNFIVHKQTDNNCWINAICLALQRLKPQWKFP
MHVPCP2 KDAFGFDEPQLLKYYTMLGMCKWPVVVCGNYFAFKQSNNNCYINVACLMLQHLSLKFPKW
TGVPCP1 QEAEQF-NPSLPPF---------KTTNLNGKIILKQGDNNCWINACCYQLQAFD--FFN-
HCVPCP1 DIETVDVKHDVSPF-------EMPFEELNGLKILKQLDNNCWVNSVMLQIQLTG--ILDG
IBVPCP DAQKYVIYLQTLAQ-------KWNVQYRDNFLILEWRDGNCWISSAIVLLQAAKIRFKG-
MHVPCP1 DAVCSEALSAFYAVPS-----DETHFKVCGFYSPAIERTNCWLRSTLIVMQSLPLEFKDL
HCVPCP2 GLDAAWNKFVLGDVEIFVAFVYYVARLMKGDKGDAEDTLTKLSKYLAN---EAQVQLEHY
TGVPCP2 GVRGLWNEFLERKTQGFVHMLYHISGVKKGEPGDAELMLHKLGDLMDN---DCEIIVTHT
MHVPCP2 QWQEAWNEFRSGKPLRFVSLVLAKGSFKFNEPSDSIDFMRVVLREADLS--GATCNLEFV
TGVPCP1 --NEAWEKFKKGDVMDFVNLCYAATTLARGHSGDAEYLLELMLNDYST----AKIVLAAK
HCVPCP1 --DYAMQFFKMGRVAKMIERCYTAEQCIRGAMGDVGLCMYRLLKDLHT----GFMVMDYK
IBVPCP FLTEAWAKLLGGDPTDFVAWCYASCTAKVGDFSDANWLLANLAEHFDADYTNAFLKKRVS
MHVPCP1 EMQKLWLSYKAGYDQCFVDKLVKSVPKSIILP-QGGYVADFAYFFLSQ---CSFKAYANW
HCVPCP2 SSCVECDAKFKNSVASINSAIVCASVKRDGVQVGYCVHGIKYYSRVRSVRGRAIIVSVEQ
TGVPCP2 TACDKCAKVEKFVGPVVAAPLAIHGTD-ET-----CVHGVSVNVKVTQIKG---TVAITS
MHVPCP2 CKCGVKQEQRKGVDAVMHFGTLDKGDLVRGYN-IACTCGSKLVHCTQFNVP----FLICS
TGVPCP1 CGCGEKEIVLERAVFKLTPLKESFNYGVCG----DCMQVNTCRFLSVEGSG-VFVHDILS
HCVPCP1 CSCTSGRLEESGAVLFCTPTKKAFPYGTCLN----CNAPRMCTIRQLQGTI--IFVQQKP
IBVPCP CNCGIKSYELRGLEACIQPVRATNLLHFKTQYS-NCPTCGANNTDEVIEASLPYLLLFAT
MHVPCP1 R-CLECDMELKLQGLDAMFFYGDVVSHMCK-----CGNSMTLLSADIPYTL----HFGVR
HCVPCP2 LEPCAQSRLLSGVAYTAFSGPVDKGHYT---------VYDTAKKSMYDGDRFVKHDLSLL
TGVPCP2 LIGPIIGEVLEATGYICYSGSNRNGHYT---------YYDNRNGLVVDAEKAYHFNRDLL
MHVPCP2 NTPEGRKLPDDVVAANIFTGG-SVGHYTHVKCKPKYQLYDACNVNKVSEAKGNFTDCLYL
TGVPCP1 KQTPEAMFVVKPVMHAVYTGTTQNGHYM---------VDDIEHGYCVDGMGIKPLKKRCY
HCVPCP1 EPVNPVSFVVKPVCSSIFRGAVSCGHYQ---------TNIYSQNLCVDGFGVNKIQPWTN
IBVPCP DGPATVDCDEDAVGTVVFVGSTNSGHCYT-------QAAGQAFDNLAKDRKFGKKSPYIT
MHVPCP1 DDKFCAFYTPRKVFRAACAVDVNDCHSMA-------VVEGKQIDGKVVTKFIGDKFDFMV
HCVPCP2 S----VTSVVMVGGYVAP-----------VNTVKPKPVINQ--
TGVPCP2 Q----VTTAIASNFVVKKPQAEERPKNCAFNKVAASPKIVQ--
MHVPCP2 KNLKQTFSSVLTTFYLDD-----------VKCVEYKPDLSQ--
TGVPCP1 TSTLFINANVMTRAEKPKQ--E-----FKVEKVEQQPIVEE--
HCVPCP1 D---ALNTICIKDADYNA-----------KVEISVTPIKN---
IBVPCP AMYTRFAFKNETSLPVAK------------QSKGKSKSVKE--
MHVPCP1 G---YGMTFSMSPFELAQ-----------LYGSCITPNVCFVK
Most important alignment rules and typical errors:
1. Different sequences should have different names.
2. Empty symbols aren't advisory inside sequence name.
3. Several blanks are advisory between sequence and its name.
4. Empty lines are mandatory inside parts of alignment.
5. Gap symbol must be '-'.
6. Beginning and finishing gaps are necessary.