User:Eric Martz/Sandbox 13: Difference between revisions

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 <font style="font-size:180%;">Sequence Alignment Tools</font>
+<font style="font-size:140%;">Notes below were made in 2011. In 2016 I met my wishes by creating [http://msareveal.org MSAReveal.Org]. Please give it a try!</font>
 What I want:
-*% identity vs. length of each chain and number of identical residues/chain length for each chain
+# % identity vs. length of each chain and number of identical residues/chain length for each chain
-*colors that indicate identity/similarity/difference
+# colors that indicate identity/similarity/difference
-*ability to block a region of the alignment and get identity and length for that region (could cut and paste a new job ...)
+# ability to block a region of the alignment and get identity and length for that region (could cut and paste a new job ...)
+== Uniprot.org ==
+*no % ident
+*gray colors
+== Jalview ==
+Seems to be mostly an alignment ''editing'' tool.
+== ClustalW2 at EBI ==
+[http://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2]
+*has colors but no color key
+*no % id (?!)
+*give a ''score'' but doesn't explain it.
+== RCSB 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-Model ==
-Jalview: seems to be mostly an alignment ''editing'' tool.
+Why doesn't it make a model of FlgE CamJe using 1wlg?
-EBI Clustal
+<pre>
+>tr|Q83WM5|Q83WM5_CAMJE FlgE OS=Campylobacter jejuni GN=flgE PE=4 SV=1
+MMRSLWSGVSGLQAHQVAMDVEGNNISNVNTTGFKYSRADFGTMFSQTVKIATAPTDGRG
+GSNPLQIGLGVSVSSTTRIHSQGSVQTTDKNTDVAINGDGFFMVSDDGGLTRYLTRSGDF
+KLDAYGNFVNNAGFVVQGWNINWDTQSIDSSRTPQNIFIDPGMHIPAAKSTEVAIKANLN
+SGLSVGTAKTPIYGLDSVHGFNKKDGTAKNENDTGITQFYTTSKNSVEVTEKGVDCAALF
+NGKGDGLNLRDGQGIWVSYADSKFSTDVPNGVNVFNPNTQATQNGVIFWGDENNAVNLDI
+TLNGVRIQNNSIKSLDQAIEYINTFTAPTDTREGTGVKAVRKADGSGIEFINTNADGTTD
+NMKNIDLVVNQANTAGERHNLTWQANNNSFQATSRKQGANSVWIPGNNPVNGTERIQIVT
+AHKYVYSSTPVQLDPMYNPDGGPAFNQANINTPGTAENNYRNAVNGSLLNTTVRTFRTTE
+DLRELLQRDARYGVDYDGSGGFEADGSDVNEGVKVTVGATGEFIISNPNVQSTPPNGIVQ
+NNRRPHDISFNVTAYTDAKGKVSTNMAFTNIFKGFDGVLTVGNSNRQSEQLFLSAFSAGL
+EIYDSLGSKHTLEVQFVKQSTTQDGGNEWQMIIRVPEPAEINTTGEGPNNIIVGTARFNN
+DGSLANYSPKTINFSPNNGAAPNQQIKLSFGTSGSNDGLVSSNSASTLTGQATDGYTSGN
+LKPDAIRVDDKGNILGEFTNGKTFAVAKMAMASVANNSGLEEIGGNLFKVTANSGAIVVG
+EAGTGGRGEMKTSALEMSNVDLSRSLTELIIIQRGYQANSKTISTSDQMLQTLIQLKQ
+>sp|P0A1J1|FLGE_SALTY Flagellar hook protein flgE OS=Salmonella typhimurium GN=flgE PE=1 SV=2
+MSFSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTASFADMFAGSKVGLGVKVAGITQD
+FTDGTTTNTGRGLDVAISQNGFFRLVDSNGSVFYSRNGQFKLDENRNLVNMQGMQLTGYP
+ATGTPPTIQQGANPAPITIPNTLMAAKSTTTASMQINLNSTDPVPSKTPFSVSDADSYNK
+KGTVTVYDSQGNAHDMNVYFVKTKDNEWAVYTHDSSDPAATAPTTASTTLKFNENGILES
+GGTVNITTGTINGATAATFSLSFLNSMQQNTGANNIVATNQNGYKPGDLVSYQINNDGTV
+VGNYSNEQEQVLGQIVLANFANNEGLASQGDNVWAATQASGVALLGTAGSGNFGKLTNGA
+LEASNVDLSKELVNMIVAQRNYQSNAQTIKTQDQILNTLVNLR
+</pre>