260 lines
7 KiB
Text
260 lines
7 KiB
Text
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Blastn (Nucleic Acid)
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itemmethod:(echo PROGRAM blastn > in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo HISTOGRAM $PLOT >> in1.tmp; echo ALIGNMENTS $SCORE >> in1.tmp; echo SPLIT 100000 >> in1.tmp; echo BEGIN >> in1.tmp; readseq -i1 -p -f8 in1 >> in1.tmp; cat in1.tmp | /bin/mail blast@ncbi.nlm.nih.gov; rm in1 in1.tmp) &
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arg:DBASE
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argtype:choice_menu
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arglabel:Which Database?
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argchoice:Non-redundant database:nr
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argchoice:GenBank DNA sequence database:genbank
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argchoice:GenBank update (cumulative daily updates):gbupdate
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argchoice:EMBL DNA sequence database:embl
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argchoice:EMBL update (cumulative weekly updates):emblu
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argchoice:Vector subset of GenBank:vector
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argchoice:Database of Expressed Sequence Tags (ESTs):dbest
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argchoice:Eukaryotic promoterdatabase:epd
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argchoice:Kabat's database of immunological interest:kabatnuc
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arg:PLOT
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argtype:chooser
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arglabel:Display Histogram?
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argvalue:1
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argchoice:Yes:yes
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argchoice:No:no
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arg:SCORE
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argtype:slider
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arglabel:Number of High Scoring Pairs Displayed?
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argmin:1
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argmax:250
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argvalue:5
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in:in1
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informat:genbank
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insave:
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item:Blastp (Protein)
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itemmethod:(echo PROGRAM blastp >in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo HISTOGRAM $PLOT >> in1.tmp; echo ALIGNMENTS $SCORE >> in1.tmp; echo MATRIX $MATRX >> in1.tmp; echo SPLIT 100000 >> in1.tmp; echo BEGIN >> in1.tmp; readseq -i1 -p -f8 in1 >> in1.tmp; cat in1.tmp | /bin/mail blast@ncbi.nlm.nih.gov; rm in1 in1.tmp) &
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arg:DBASE
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argtype:choice_menu
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arglabel:Which Database?
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argchoice:Non-redundant protein database:nr
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argchoice:Swiss-Prot protein database:swissprot
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argchoice:PIR protein database:pir
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argchoice:Cumulative update to Swiss-Prot major release:spupdate
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argchoice:GenPept (translated GenBank):genpept
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argchoice:GenPept update (cumulative daily updates):gpupdate
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argchoice:Brookhaven PDB:pdb
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argchoice:Kabat's database of immunological interest:kabatnuc
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argchoice:Transcription Factors Database:tfd
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argchoice:6-frame translations of human Alu repeats:palu
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arg:PLOT
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argtype:chooser
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arglabel:Display Histogram?
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argvalue:1
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argchoice:Yes:yes
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argchoice:No:no
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arg:SCORE
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argtype:slider
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arglabel:Number of High Scoring Pairs Displayed
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argmin:1
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argmax:250
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argvalue:5
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arg:Matrx
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argtype:chooser
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arglabel:Weighting matrix
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argchoice:PAM 250:PAM250
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argchoice:PAM 120:PAM10
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argchoice:PAM 40:PAM40
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argchoice:BLOSUM62:BLOSUM62
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in:in1
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informat:genbank
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insave:
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item:Fasta (Nucleic Acid)
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itemmethod:(echo LIB $DBASE > in1.tmp; echo WORD $KPL >> in1.tmp; echo LIST $TOP >> in1.tmp; echo ALIGN $ALNG >> in1.tmp; echo ONE >> in1.tmp; echo SEQ >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp;Mail FASTA@EMBL-Heidelberg.de < in1.tmp; rm in1 in1.tmp) &
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arg:DBASE
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argtype:choice_menu
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arglabel:Which Database?
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argchoice:GenBank Qrtly & Updates:GBALL
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argchoice:GenBank Updates:GBNEW
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argchoice:Entries only in GenBank, not in EMBL:GBONLY
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argchoice:GenBank and EMBL entries (latest releases):GENEMBL
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argchoice:New EMBL entries (Since latest release):EMNEW
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argchoice:All EMBL entries (latest release + new ones):EMALL
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argchoice:EMBL fungi division only:EFUN
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argchoice:EMBL invertebrates division only:EINV
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argchoice:EMBL mammals division only:EMAM
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argchoice:EMBL organelles division only:EORG
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argchoice:EMBL phages division only:EPHG
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argchoice:EMBL plants division only:EPLN
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argchoice:EMBL primates division only:EPRI
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argchoice:EMBL prokaryotes division only:EPRO
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argchoice:EMBL rodents division only:EROD
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argchoice:EMBL synthetic sequences division only:ESYN
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argchoice:EMBL unannotated division only:EUNA
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argchoice:EMBL viruses division only:EVRL
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argchoice:EMBL vertebrates division only:EVRT
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arg:KPL
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argtype:slider
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arglabel:K-tuple window
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argmin:3
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argmax:6
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argvalue:4
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arg:TOP
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argtype:slider
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arglabel:Scores Displayed?
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argmin:1
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argmax:200
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argvalue:100
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arg:ALNG
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argtype:slider
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arglabel:# Alignments Displayed?
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argmin:1
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argmax:200
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argvalue:20
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in:in1
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informat:flat
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insave:
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item:Fasta (Protein)
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itemmethod:(echo LIB $DBASE > in1.tmp; echo WORD $TPL >> in1.tmp; echo LIST $SCRS >> in1.tmp; echo ALIGN $ALNMNTS >> in1.tmp; echo PROT >> in1.tmp; echo SEQ >> in1.tmp; sed "s/-//g" < in1 | tr '@%#$' '>' >> in1.tmp; Mail FASTA@EMBL-Heidelberg.de < in1.tmp; rm in1 in1.tmp) &
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arg:DBASE
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argtype:choice_menu
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arglabel:Which Protein Database?
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argchoice:Swiss-Protein (latest release + new ones):SWALL
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argchoice:Swiss-Protein (since latest release):SWNEW
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argchoice:Swiss-Protein (latest release):SW
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argchoice:NBRF/PIR (latest release):NBRF
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argchoice:NBRF/PIR (not Swiss-Prot):PIRONLY
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argchoice:All Swiss-Prot and NBRF/PIR entries:SWISSPIRALL
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argchoice:PDB structure entries:BROOKHAVEN
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argchoice:PDB structure entries (NBRF version):NRL
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arg:TPL
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argtype:slider
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arglabel:K-TUP window
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argmin:1
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argmax:2
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argvalue:1
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arg:SCRS
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argtype:slider
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arglabel:# Scores Displayed?
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argmin:1
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argmax:200
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argvalue:100
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arg:ALNMNTS
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argtype:slider
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arglabel:# Alignments Displayed?
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argmin:1
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argmax:200
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argvalue:20
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in:in1
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informat:flat
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insave:
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item:GeneID
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itemmethod:($REPRINT > in1.tmp; echo Genomic Sequence >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail geneid@darwin.bu.edu < in1.tmp; rm in1 in1.tmp) &
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arg:REPRINT
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argtype:chooser
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arglabel:Do you want a GENEID reprint?
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argchoice:YES:echo "Preprint Request" >> in1.tmp
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argchoice:NO
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in:in1
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informat:flat
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insave:
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item:Sequence Retrieval
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itemmethod:(echo DATALIB $DBASE>> in1.tmp; echo MAXDOCS $NDOC >> in1.tmp;echo MAXLINES 100000 >> in1.tmp; echo BEGIN >> in1.tmp; echo $REGEXP >> in1.tmp; Mail retrieve@ncbi.nlm.nih.gov < in1.tmp; rm in1.tmp) &
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arg:DBASE
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argtype:choice_menu
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arglabel:Which Database?
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argchoice:GenBank DNA sequence database:genbank
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argchoice:GenBank update (cumulative daily updates):gbupdate
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argchoice:EMBL DNA sequence database:embl
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argchoice:EMBL update (cumulative weekly updates):emblu
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argchoice:Vector subset of GenBank:vector
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argchoice:Database of Expressed Sequence Tags (ESTs):dbest
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argchoice:Swiss-Prot protein database:swissprot
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argchoice:PIR protein database:pir
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argchoice:GenPept (translated GenBank):genpept
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argchoice:GenPept update (cumulative daily updates):gpupdate
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argchoice:Transcription Factors Database:tfd
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arg:NDOC
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argtype:slider
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arglabel:Number of Sequences Retrieved?
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argmin:1
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argmax:100
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argvalue:20
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arg:REGEXP
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argtype:text
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arglabel:key words, sequence IDs, boolean connectors
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item:Grail
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itemmethod:(echo Sequences $TOTALSEQS $ID > in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail grail@ornl.gov <in1.tmp; rm in1 in1.tmp) &
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arg:REGISTER
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argtype:chooser
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arglabel:Have you previously registered for Grail services?
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argchoice:YES
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argchoice:NO:echo "YOU MUST REGISTER"
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arg:TOTALSEQS
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argtype:text
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arglabel:Number of Sequences Being Sent to Grail?
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arg:ID
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argtype:text
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arglabel:User ID (MUST HAVE PREVIOUSLY REGISTERED)
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in:in1
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informat:flat
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insave:
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item:Grail Registration
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itemmethod:(echo Register > in1.tmp; echo $NAME >> in1.tmp; echo $ADDRESS >> in1.tmp; echo $PHONE >> in1.tmp; echo $EMAIL >> in1.tmp; Mail grail@ornl.gov < in1.tmp; rm in1.tmp)
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arg:NAME
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argtype:text
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arglabel:Your Name
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arg:ADDRESS
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argtype:text
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arglabel:Your Address
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arg:PHONE
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argtype:text
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arglabel:Your Phone Number
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arg:EMAIL
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argtype:text
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arglabel:Your E-Mail Address
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