Difference between revisions of "Metachromatic leukodystrophy reference aminoacids"
| Line 37: | Line 37: | ||
==== How To ==== |
==== How To ==== |
||
fasta was not yet installed on the computer, so it was installed, executing the following command from the ./src directory from the software's sourc code: |
fasta was not yet installed on the computer, so it was installed, executing the following command from the ./src directory from the software's sourc code: |
||
| − | make -f ../make/Makefile.linux_sse2 all |
+ | * <code>make -f ../make/Makefile.linux_sse2 all</code> |
We aligned the sequences, using the parameters written below: |
We aligned the sequences, using the parameters written below: |
||
| − | ./bin/fasta36 -q ~/Documents/refSeq.fasta /data/blast/nr/nr > fasta_results.txt |
+ | * <code>./bin/fasta36 -q ~/Documents/refSeq.fasta /data/blast/nr/nr > fasta_results.txt </code> |
=== hhsearch === |
=== hhsearch === |
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Revision as of 09:31, 21 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, executing the following command from the ./src directory from the software's sourc code:
make -f ../make/Makefile.linux_sse2 all
We aligned the sequences, using the parameters written below:
./bin/fasta36 -q ~/Documents/refSeq.fasta /data/blast/nr/nr > fasta_results.txt
hhsearch
How To
We used the online version of hhPred <ref>http://toolkit.lmb.uni-muenchen.de/hhpred</ref> with the following parameters
- global alignment
- 3 iterations
against PDB
against InterPro
References
<references />
