DAP intro: Difference between revisions
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== Blastp == | == Blastp == | ||
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*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''' | '''>gi|119390187|pdb|2IJZ|A Chain A, Crystal Structure Of Aminopeptidase''' | ||
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FYASSELP | 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 | C:\blast\blastall -p blastp -d C:\blast\databases\nr -i yourfile.fasta -o usefuloutputname.html | ||
Output obtained : file:///C:/aminopeptidase.html | Output obtained : file:///C:/aminopeptidase.html | ||
Revision as of 04:32, 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
Output obtained : file:///C:/aminopeptidase.html
