DAP method: Difference between revisions
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ref|NP_956447.1| | ref|NP_956447.1| | ||
Changed headings in every single obtained fasta sequences, e.g : | Changed headings in every single obtained fasta sequences into organism names only, e.g : | ||
'''From ''' | |||
'''<nowiki>>gi|116051260|ref|YP_789908.1| putative aminopeptidase 2 [Pseudomonas aeruginosa UCBPP-PA14]</nowiki>''' | |||
MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTEAGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVG | |||
AHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRA | |||
ANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLS | |||
CHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADK | |||
DANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAM | |||
HSIRELAGSHDLAHLVKVLGAFYASSELP | |||
'''To''' | |||
'''>Pseudomonas_aeruginosa''' | |||
MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTEAGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVG | |||
AHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRA | |||
ANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLS | |||
CHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADK | |||
DANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAM | |||
HSIRELAGSHDLAHLVKVLGAFYASSELP | |||
saved into a new file organismnames.fasta |
Revision as of 08:20, 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 into organism names only, e.g :
From
>gi|116051260|ref|YP_789908.1| putative aminopeptidase 2 [Pseudomonas aeruginosa UCBPP-PA14]
MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTEAGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVG
AHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRA
ANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLS
CHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADK
DANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAM
HSIRELAGSHDLAHLVKVLGAFYASSELP
To
>Pseudomonas_aeruginosa
MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTEAGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVG
AHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRA
ANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLS
CHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADK
DANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAM
HSIRELAGSHDLAHLVKVLGAFYASSELP
saved into a new file organismnames.fasta