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