User:Eric Martz/Sandbox 13

Sequence Alignment Tools

What I want:

1. % identity vs. length of each chain and number of identical residues/chain length for each chain
2. colors that indicate identity/similarity/difference
3. ability to block a region of the alignment and get identity and length for that region (could cut and paste a new job ...)

Uniprot.orgUniprot.org

• no % ident
• gray colors

JalviewJalview

Seems to be mostly an alignment editing tool.

ClustalW2 at EBIClustalW2 at EBI

ClustalW2

• has colors but no color key
• no % id (?!)
• give a score but doesn't explain it.

RCSB Compare StructuresRCSB Compare Structures

• Smith-Waterman or Needleman-Wunsch does #1,#2 but only for sequences of 3D structures.
• Smith-Waterman shows only the aligned segments, while Needleman-Wunsch shows full length with gaps.

Swiss-ModelSwiss-Model

Why doesn't it make a model of FlgE CamJe using 1wlg?

>tr|Q0P7Q2|Q0P7Q2_CAMJE Flagellar hook subunit protein OS=Campylobacter jejuni GN=flgE2 PE=1 SV=1
MMRSLWSGVSGLQAHQVAMDVEGNNISNVNTTGFKYSRADFGTMFSQTVKIATAPTDGRG
GSNPLQIGLGVSVSSTTRIHSQGSVQTTDKNTDVAINGDGFFMVSDDGGLTNYLTRSGDF
KLDAYGNFVNNAGFVVQGWNINWDDQTIDSSRTPQNIFIDPGMHIPAAKSTEVAIKANLN
SGLNIGTSSRNLYALDSVHGWNTKTQRAEDENDTGTTQFYTTSKNSVEVTEKGVDAGSLF
NAKGQGLNLRDGQGIWVSYADATYSTNKVGVNAFDPNLQQNQTAAFWGTANQKVNLDITL
NGVRIQNADIQSIDDAIAYINTFTAPTDTRDGTGVKAVKNKDGSGIDFVNDNADGTTDNM
KNINLVVANTNTAGELWNAVWNNNNQTFTFNNNGNGQAGTPTINKNGSSLWTATNITFTP
QPPQAATNVQLTGGLNAQIITAHKYIYSSNPVDIGPMYNPDGGPAFQPGANATTRPTEPG
SAAYWDAVNGGLLNTNVRTFRTTEDLRELLQRDARYGVDYDGSGTFAAADINQNIKVVVT
ADGHFAISNANEQSTVPPNAINGVGNATTTDPKNMSFNITAYSNKQGTVSTNDAFTAIFK
AFDGPLVIGNQIKESEQLKLSAFSAGLEIYDSLGSKHTLEVQFVKQSTTQDGGNEWQMII
RVPEPAEINTTGEGPNNIIVGTARFNNDGSLASYTPRTINFSPNNGAAPNQQIKLSFGTS
GSNDGLVSSNSASTLTGQATDGYTSGNLKPDAIRVDDKGNILGEFTNGKTFAVAKIAMAS
VANNSGLEEIGGNLFKVTANSGNIVVGEAGTGGRGEMKTSALEMSNVDLSRSLTELIIIQ
RGYQANSKTISTSDQMLQTLIQLKQ
>sp|P0A1J1|FLGE_SALTY Flagellar hook protein flgE OS=Salmonella typhimurium GN=flgE PE=1 SV=2
MSFSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTASFADMFAGSKVGLGVKVAGITQD
FTDGTTTNTGRGLDVAISQNGFFRLVDSNGSVFYSRNGQFKLDENRNLVNMQGMQLTGYP
ATGTPPTIQQGANPAPITIPNTLMAAKSTTTASMQINLNSTDPVPSKTPFSVSDADSYNK
KGTVTVYDSQGNAHDMNVYFVKTKDNEWAVYTHDSSDPAATAPTTASTTLKFNENGILES
GGTVNITTGTINGATAATFSLSFLNSMQQNTGANNIVATNQNGYKPGDLVSYQINNDGTV
VGNYSNEQEQVLGQIVLANFANNEGLASQGDNVWAATQASGVALLGTAGSGNFGKLTNGA
LEASNVDLSKELVNMIVAQRNYQSNAQTIKTQDQILNTLVNLR