DAP method: Difference between revisions
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'''>gi|119390187|pdb|2IJZ|A Chain A, Crystal Structure Of Aminopeptidase''' | '''>gi|119390187|pdb|2IJZ|A Chain A, Crystal Structure Of Aminopeptidase''' | ||
RAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSP | |||
LESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESR | |||
LVDFRKAIAVIPNLNIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYE | |||
LSFYDTQSAAVVGLNDEFIAGARLDNLLSCHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLE | |||
QVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETA | |||
GFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGA | |||
FYASSELP | |||
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Obtained fastaformat files | Obtained fastaformat files | ||
C:\blast\fastacmd -d C:\blast\databases\nr -i filewith_img_numbers -o C:\newsequences.fasta | C:\blast\fastacmd -d C:\blast\databases\nr -i filewith_img_numbers -o C:\newsequences.fasta | ||
Inputs used for obtaining fastaformat files: | |||
pdb|2IJZ|A | |||
ref|YP_789908.1| | |||
ref|YP_261475.1| | |||
ref|ZP_00416764.1| | |||
ref|NP_743887.1| | |||
ref|NP_793647.1| | |||
ref|YP_607123.1| | |||
ref|YP_958321.1| | |||
ref|ZP_01894798.1| | |||
ref|ZP_01166960.1| | |||
ref|ZP_01738318.1| | |||
ref|YP_436072.1| | |||
ref|ZP_01462550.1| | |||
ref|YP_630602.1| | |||
ref|YP_001615044.1| | |||
ref|YP_747571.1| | |||
ref|YP_113441.1| | |||
ref|XP_001751765.1| | |||
ref|XP_001641062.1| | |||
ref|XP_713998.1| | |||
gb|AAM61631.1| | |||
ref|XP_365906.1| | |||
ref|XP_843934.1| | |||
ref|NP_001045513.1| | |||
ref|XP_001566576.1| | |||
ref|XP_001877081.1| | |||
gb|ACC64563.1| | |||
ref|XP_001492028.1| | |||
ref|NP_001039417.1| | |||
ref|YP_833603.1| | |||
ref|NP_036232.2| | |||
ref|NP_001012937.1| | |||
ref|NP_001104301.1| | |||
gb|EDL75426.1| | |||
ref|NP_001085525.1| | |||
ref|XP_462175.1| | |||
ref|NP_956447.1| | |||
Changed headings in every single obtained fasta sequences, e.g : |
Revision as of 07:57, 4 June 2008
Blastp
- FASTA SEQUENCE FROM NCBI ENTREZ protein = 2IJZ_A
- Origin of query sequence = Pseudomonas aeruginosa
>gi|119390187|pdb|2IJZ|A Chain A, Crystal Structure Of Aminopeptidase RAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSP LESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESR LVDFRKAIAVIPNLNIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYE LSFYDTQSAAVVGLNDEFIAGARLDNLLSCHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLE QVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETA GFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGA FYASSELP
- Performed blastp search against non-redundant (nr) databases which was provided on the CD provided. Query sequences used was Pseudomonas Aeruginosa chain A crystal structure of asparytl aminopeptidase.
- Initial sequence alignment was performed using ClustalX and edited to reduce gapping in the alignment and final multiple sequence alignment was again performed with 38 sequences.
- Treeview32 software was used to view phylogenetic tree produced from multiple sequence alignment and a bootstrapped N-J tree was produced using Clustalx for branches reliability indications.
As mentioned in the methods and website :
C:\blast\blastall -p blastp -d C:\blast\databases\nr -i yourfile.fasta -o usefuloutputname.html
Obtained fastaformat files
C:\blast\fastacmd -d C:\blast\databases\nr -i filewith_img_numbers -o C:\newsequences.fasta
Inputs used for obtaining fastaformat files:
pdb|2IJZ|A ref|YP_789908.1| ref|YP_261475.1| ref|ZP_00416764.1| ref|NP_743887.1| ref|NP_793647.1| ref|YP_607123.1| ref|YP_958321.1| ref|ZP_01894798.1| ref|ZP_01166960.1| ref|ZP_01738318.1| ref|YP_436072.1| ref|ZP_01462550.1| ref|YP_630602.1| ref|YP_001615044.1| ref|YP_747571.1| ref|YP_113441.1| ref|XP_001751765.1| ref|XP_001641062.1| ref|XP_713998.1| gb|AAM61631.1| ref|XP_365906.1| ref|XP_843934.1| ref|NP_001045513.1| ref|XP_001566576.1| ref|XP_001877081.1| gb|ACC64563.1| ref|XP_001492028.1| ref|NP_001039417.1| ref|YP_833603.1| ref|NP_036232.2| ref|NP_001012937.1| ref|NP_001104301.1| gb|EDL75426.1| ref|NP_001085525.1| ref|XP_462175.1| ref|NP_956447.1|
Changed headings in every single obtained fasta sequences, e.g :