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Example sentences for: ftp

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Protein secondary structure was predicted using a multiple alignment as the input for the JPRED and PHD programs [ 42 43 44 ] . Preliminary clustering of proteins was done using the BLASTCLUST program with empirically determined length and score threshold cut off values (For documentation see ftp://ftp.ncbi.nih.gov/blast/documents/README.bcl).
Completed genomes were retrieved from the NCBI's FTP site ftp://ncbi.nlm.nih.gov/genbank/genomes/in the form of amino acid sequences encoded by open reading frames (ORFs) as identified in the annotated genomes.
Repeat sequences were masked with the RepeatMasker program (RepeatMasker at http://ftp.genome.washington.edu/RM/RepeatMasker.html).
Protein secondary structure was predicted using a multiple alignment as the input for the JPRED and PHD programs [ 39 40 ] . Preliminary clustering of proteins was done using the BLASTCLUST program with empirically determined length and score threshold cut off values (For documentation see ftp://ftp.ncbi.nih.gov/blast/documents/README.bcl).
Once a sequence containing the desired polymorphism was selected (usually 400-700 bp in length), it was run through the Repeat Masker program http://ftp.genome.washington.edu/cgi-bin/RepeatMaskerin order to avoid selecting PCR primers within Alu, L1, or other repeats.