User:Eric Martz/Sandbox 13: Difference between revisions
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Uniprot.org
Jalview
ClustalW2 at EBI
RCSB Compare Structures
Swiss-Model
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
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# 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 22: | ||
*no % id (?!) | *no % id (?!) | ||
*give a ''score'' but doesn't explain it. | *give a ''score'' but doesn't explain it. | ||
| Line 23: | Line 28: | ||
*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|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 | |||
</pre> | |||
Revision as of 08:58, 25 May 2011
Sequence Alignment Tools
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 ...)
Uniprot.orgUniprot.org
- no % ident
- gray colors
JalviewJalview
Seems to be mostly an alignment editing tool.
ClustalW2 at EBIClustalW2 at EBI
- 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