User:Eric Martz/Sandbox 13
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<font style="font-size:180%;">Sequence Alignment Tools</font> | <font style="font-size:180%;">Sequence Alignment Tools</font> | ||
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| + | <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> | ||
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What I want: | What I want: | ||
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# 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 ...) | ||
| - | Jalview: seems to be mostly an alignment ''editing'' tool. | ||
| - | EBI Clustal | ||
| - | RCSB Compare Structures | + | == 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. | ||
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| + | |||
| + | == Swiss-Model == | ||
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| + | 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> | ||
Current revision
Sequence Alignment Tools
Notes below were made in 2011. In 2016 I met my wishes by creating MSAReveal.Org. Please give it a try!
What I want:
- % identity vs. length of each chain and number of identical residues/chain length for each chain
- 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 ...)
Contents |
Uniprot.org
- no % ident
- gray colors
Jalview
Seems to be mostly an alignment editing tool.
ClustalW2 at EBI
- 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
Why doesn't it make a model of FlgE CamJe using 1wlg?
>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
