Difference between revisions of "Talk:Make"
From Christoph's Personal Wiki
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A list of random make/gmake/shell commands: | A list of random make/gmake/shell commands: | ||
| − | == | + | == DSSP == |
* CPH -> RSCB -> ALIGNAA -> JNET | * CPH -> RSCB -> ALIGNAA -> JNET | ||
* Fasta file containing all pdb entries (pdb): <nowiki>ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z</nowiki> | * Fasta file containing all pdb entries (pdb): <nowiki>ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z</nowiki> | ||
Revision as of 23:21, 17 October 2006
A list of random make/gmake/shell commands:
DSSP
- CPH -> RSCB -> ALIGNAA -> JNET
- Fasta file containing all pdb entries (pdb): ftp://ftp.ncbi.nih.gov/blast/db/pdbaa.Z
- Non-redundant database of known protein sequences (sp) compiled from files: ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/fasta/*.fas.gz (Swiss-prot)
- PDB entries: ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/
%.cph.fa: %.cph
for pdbid in $$(cat $< | gawk '{print $$2}' | sort | uniq);
do wget http://www.rcsb.org/pdb/files/$$pdbid.pdb.gz;
done
wait
for pdbid in *.gz; do gunzip $$pdbid; done
for pdbid in $$(for pdbid in *.pdb; do basename $$pdbid .pdb; done);
do gmake $$pdbid.fa;
done
for pdbid in *.fa;
do perl multi_alignaa.pl $(shell basename $< .cph).fa $$pdbid >> $@;
done
