Metachromatic leukodystrophy reference aminoacids

From Bioinformatikpedia
Revision as of 09:30, 21 May 2011 by Zacher (talk | contribs)

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

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 />