Difference between revisions of "Metachromatic leukodystrophy reference aminoacids"
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==== How To ==== |
==== How To ==== |
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With BLAST being installed, the following steps were performed: |
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 |
|
==== Best 20 results ==== |
==== Best 20 results ==== |
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| Line 28: | Line 28: | ||
==== How To ==== |
==== How To ==== |
||
With PSI-BLAST being installed, the following steps were performed: |
With PSI-BLAST being installed, the following steps were performed: |
||
| − | + | * typed <code>blastpgp -i refSeq.fasta -d /data/blast/nr/nr -e"e-value" -j "#iterations" > psiblast_"e-value"_"#iterations"</code> |
|
==== e-value cutoff 0.005, 3 iterations ==== |
==== e-value cutoff 0.005, 3 iterations ==== |
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==== e-value cutoff 0.005, 5 iterations ==== |
==== e-value cutoff 0.005, 5 iterations ==== |
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=== FASTA against NR === |
=== FASTA against NR === |
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| + | ==== How To ==== |
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fasta was not yet installed on the computer, so it was installed in the following way: |
fasta was not yet installed on the computer, so it was installed in the following way: |
||
Revision as of 16:01, 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 > blastpwith 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
How To
fasta was not yet installed on the computer, so it was installed in the following way:
