Difference between revisions of "Metachromatic leukodystrophy reference aminoacids"
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TAHEPPLLYDLSKDPGENYNLLGGVAGATPEVLQALKQLQLLKAQLDAAVTFGPSQVARG<br/> |
TAHEPPLLYDLSKDPGENYNLLGGVAGATPEVLQALKQLQLLKAQLDAAVTFGPSQVARG<br/> |
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EDPALQICCHPGCTPRPACCHCPDPHA</code> |
EDPALQICCHPGCTPRPACCHCPDPHA</code> |
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== Source == |
== Source == |
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*[http://www.uniprot.org/uniprot/P15289.fasta Uniprot] |
*[http://www.uniprot.org/uniprot/P15289.fasta Uniprot] |
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| + | |||
| + | |||
| + | == Database Searches == |
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| + | |||
| + | === BLAST against NR === |
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| + | ==== How To ==== |
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| + | With BLAST being installed, the following steps were performed: |
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| + | - typed <code>blastall -p blastp -i refSeq.fasta -d /data/blast/nr/nr > blastp</code> with refSeq.fasta being the file containing the reference sequence and blastp the outfile |
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| + | ==== Best 20 results ==== |
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| + | |||
| + | |||
| + | === PSI-BLAST against NR === |
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| + | ==== How To ==== |
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| + | With PSI-BLAST being installed, the following steps were performed: |
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| + | - typed <code>blastpgp -i refSeq.fasta -d /data/blast/nr/nr -e"e-value" -j "#iterations" > psiblast_"e-value"_"#iterations"</code> |
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| + | ==== e-value cutoff 0.005, 3 iterations ==== |
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| + | ==== e-value cutoff 0.005, 5 iterations ==== |
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| + | ==== e-value cutoff 10E-6, 3 iterations ==== |
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| + | ==== e-value cutoff 10E-6, 5 iterations ==== |
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| + | |||
| + | === FASTA against NR === |
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| + | fasta was not yet installed on the computer, so it was installed in the following way: |
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| + | |||
| + | === hhsearch against PDB === |
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Revision as of 16:52, 19 May 2011
Contents
Sequence
>sp|P15289|ARSA_HUMAN Arylsulfatase A OS=Homo sapiens GN=ARSA PE=1 SV=3
MGAPRSLLLALAAGLAVARPPNIVLIFADDLGYGDLGCYGHPSSTTPNLDQLAAGGLRFT
DFYVPVSLCTPSRAALLTGRLPVRMGMYPGVLVPSSRGGLPLEEVTVAEVLAARGYLTGM
AGKWHLGVGPEGAFLPPHQGFHRFLGIPYSHDQGPCQNLTCFPPATPCDGGCDQGLVPIP
LLANLSVEAQPPWLPGLEARYMAFAHDLMADAQRQDRPFFLYYASHHTHYPQFSGQSFAE
RSGRGPFGDSLMELDAAVGTLMTAIGDLGLLEETLVIFTADNGPETMRMSRGGCSGLLRC
GKGTTYEGGVREPALAFWPGHIAPGVTHELASSLDLLPTLAALAGAPLPNVTLDGFDLSP
LLLGTGKSPRQSLFFYPSYPDEVRGVFAVRTGKYKAHFFTQGSAHSDTTADPACHASSSL
TAHEPPLLYDLSKDPGENYNLLGGVAGATPEVLQALKQLQLLKAQLDAAVTFGPSQVARG
EDPALQICCHPGCTPRPACCHCPDPHA
Source
Database Searches
BLAST against NR
How To
With BLAST being installed, the following steps were performed:
- typed blastall -p blastp -i refSeq.fasta -d /data/blast/nr/nr > blastp with refSeq.fasta being the file containing the reference sequence and blastp the outfile
Best 20 results
PSI-BLAST against NR
How To
With PSI-BLAST being installed, the following steps were performed:
- typed blastpgp -i refSeq.fasta -d /data/blast/nr/nr -e"e-value" -j "#iterations" > psiblast_"e-value"_"#iterations"
e-value cutoff 0.005, 3 iterations
e-value cutoff 0.005, 5 iterations
e-value cutoff 10E-6, 3 iterations
e-value cutoff 10E-6, 5 iterations
FASTA against NR
fasta was not yet installed on the computer, so it was installed in the following way:
