Difference between revisions of "Metachromatic leukodystrophy reference aminoacids"
Line 27: | Line 27: | ||
=== PSI-BLAST against NR === |
=== PSI-BLAST against NR === |
||
==== How To ==== |
==== How To ==== |
||
− | With PSI-BLAST being installed, the following |
+ | With PSI-BLAST being installed, the following command was executed: |
− | * |
+ | * <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 ==== |
||
+ | ===== Best 20 results ===== |
||
==== e-value cutoff 0.005, 5 iterations ==== |
==== e-value cutoff 0.005, 5 iterations ==== |
||
+ | ===== Best 20 results ===== |
||
==== e-value cutoff 10E-6, 3 iterations ==== |
==== e-value cutoff 10E-6, 3 iterations ==== |
||
+ | ===== Best 20 results ===== |
||
==== e-value cutoff 10E-6, 5 iterations ==== |
==== e-value cutoff 10E-6, 5 iterations ==== |
||
+ | ===== Best 20 results ===== |
||
=== FASTA against NR === |
=== FASTA against NR === |
||
Line 49: | Line 53: | ||
Due to the fact that only PDB-IDs could be extracted from the HHpred-output, we had to do a mapping from PDB ID to RefSeq AC. This was done by mapping PDB ID to UniProt AC and then to RefSeq AC by PIR ID Mapping <ref>http://pir.georgetown.edu/pirwww/search/idmapping.shtml</ref> |
Due to the fact that only PDB-IDs could be extracted from the HHpred-output, we had to do a mapping from PDB ID to RefSeq AC. This was done by mapping PDB ID to UniProt AC and then to RefSeq AC by PIR ID Mapping <ref>http://pir.georgetown.edu/pirwww/search/idmapping.shtml</ref> |
||
==== against PDB ==== |
==== against PDB ==== |
||
− | ==== |
+ | ===== Best 20 results ===== |
+ | |||
+ | == Multiple Alignments == |
||
+ | For building the multiple Alignments the results of the Psiblast run with e-value cutoff of 10E-6 and 5 iterations were divided into 6 groups by sequence identity: |
||
+ | * <20% |
||
+ | * 20% - 39% |
||
+ | * 40% - 59% |
||
+ | * 60% - 89% |
||
+ | * 90% - 99% |
||
+ | * >99% |
||
Revision as of 14:34, 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 > 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 command was executed:
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
Best 20 results
e-value cutoff 0.005, 5 iterations
Best 20 results
e-value cutoff 10E-6, 3 iterations
Best 20 results
e-value cutoff 10E-6, 5 iterations
Best 20 results
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
- local alignment
- 3 iterations
Due to the fact that only PDB-IDs could be extracted from the HHpred-output, we had to do a mapping from PDB ID to RefSeq AC. This was done by mapping PDB ID to UniProt AC and then to RefSeq AC by PIR ID Mapping <ref>http://pir.georgetown.edu/pirwww/search/idmapping.shtml</ref>
against PDB
Best 20 results
Multiple Alignments
For building the multiple Alignments the results of the Psiblast run with e-value cutoff of 10E-6 and 5 iterations were divided into 6 groups by sequence identity:
- <20%
- 20% - 39%
- 40% - 59%
- 60% - 89%
- 90% - 99%
- >99%
References
<references />