User:Eric Martz/Sandbox 13: Difference between revisions
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
<font style="font-size:180%;">Sequence Alignment Tools</font> | <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: | What I want: | ||
| Line 5: | Line 9: | ||
# 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 | |||
| Line 16: | Line 26: | ||
*no % id (?!) | *no % id (?!) | ||
*give a ''score'' but doesn't explain it. | *give a ''score'' but doesn't explain it. | ||
| Line 23: | Line 32: | ||
*Smith-Waterman shows only the aligned segments, while Needleman-Wunsch shows full length with gaps. | *Smith-Waterman shows only the aligned segments, while Needleman-Wunsch shows full length with gaps. | ||
Swiss-Model | |||
== Swiss-Model == | |||
Why doesn't it make a model of FlgE CamJe using 1wlg? | Why doesn't it make a model of FlgE CamJe using 1wlg? | ||
<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> | |||