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: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 6: Line 10:
# 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: Smith-Waterman does #1 but only for sequences of 3D 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.
 
 
== Swiss-Model ==
 
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>

Latest revision as of 19:53, 21 February 2017

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:

  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|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
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