C.2. Datatype-specific Qualifiers

C.2.1. Sequence Input

Table C.2. Sequence Reading Qualifiers
ACD datatypeQualifierDescriptionDefault value

sequence

-sbegin integer

Start of the sequence to be used

0

-send integer

End of the sequence to be used

0

-sreverse Y/N

Reverse (if DNA)

N

-sask Y/N

Ask for begin/end/reverse

N

-snucleotide Y/N

Sequence is nucleotide

N

-sprotein Y/N

Sequence is protein

N

-slower Y/N

Make lower case

N

-supper Y/N

Make upper case

N

-sformat string

Input sequence format

""

-sdbname string

Database name

""

-sid string

Entryname

""

-ufo string

UFO features

""

-fformat string

Features format

""

-fopenfile string

Features file name

""

seqall

-sbegin integer

Start of each sequence to be used

0

-send integer

End of each sequence to be used

0

-sreverse Y/N

Reverse (if DNA)

N

-sask Y/N

Ask for begin/end/reverse

N

-snucleotide Y/N

Sequence is nucleotide

N

-sprotein Y/N

Sequence is protein

N

-slower Y/N

Make lower case

N

-supper Y/N

Make upper case

N

-sformat string

Input sequence format

""

-sdbname string

Database name

""

-sid string

Entryname

""

-ufo string

UFO features

""

-fformat string

Features format

""

-fopenfile string

Features file name

""

seqset

-sbegin integer

Start of each sequence to be used

0

-send integer

End of each sequence to be used

0

-sreverse Y/N

Reverse (if DNA)

N

-sask Y/N

Ask for begin/end/reverse

N

-snucleotide Y/N

Sequence is nucleotide

N

-sprotein Y/N

Sequence is protein

N

-slower Y/N

Make lower case

N

-supper Y/N

Make upper case

N

-sformat string

Input sequence format

""

-sdbname string

Database name

""

-sid string

Entryname

""

-ufo string

UFO features

""

-fformat string

Features format

""

-fopenfile string

Features file name

""

seqsetall

-sbegin integer

Start of each sequence to be used

0

-send integer

End of each sequence to be used

0

-sreverse Y/N

Reverse (if DNA)

N

-sask Y/N

Ask for begin/end/reverse

N

-snucleotide Y/N

Sequence is nucleotide

N

-sprotein Y/N

Sequence is protein

N

-slower Y/N

Make lower case

N

-supper Y/N

Make upper case

N

-sformat string

Input sequence format

""

-sdbname string

Database name

""

-sid string

Entryname

""

-ufo string

UFO features

""

-fformat string

Features format

""

-fopenfile string

Features file name

""

C.2.2. Sequence Output

Table C.3. Sequence Writing Qualifiers.
ACD datatypeQualifierDescriptionDefault value

seqout

-osformat string

Output seq format

""

-osextension string

File name extension

""

-osname string

Base file name

""

-osdirectory string

Output directory

""

-osdbname string

Database name to add

""

-ossingle Y/N

Separate file for each entry

N

-oufo string

UFO features

""

-offormat string

Features format

""

-ofname string

Features file name

""

-ofdirectory string

Output directory

""

seqoutall

-osformat string

Output seq format

""

-osextension string

File name extension

""

-osname string

Base file name

""

-osdirectory string

Output directory

""

-osdbname string

Database name to add

""

-ossingle Y/N

Separate file for each entry

N

-oufo string

UFO features

""

-offormat string

Features format

""

-ofname string

Features file name

""

-ofdirectory string

Output directory

""

seqoutset

-osformat string

Output seq format

""

-osextension string

File name extension

""

-osname string

Base file name

""

-osdirectory string

Output directory

""

-osdbname string

Database name to add

""

-ossingle Y/N

Separate file for each entry

N

-oufo string

UFO features

""

-offormat string

Features format

""

-ofname string

Features file name

""

-ofdirectory string

Output directory

""

C.2.3. Features

Table C.4. Feature Qualifiers
ACD datatypeQualifierDescriptionDefault value

features

-fformat string

Features format

""

-fopenfile string

Features file name

""

-fask Y/N

Prompt for begin/end/reverse

N

-fbegin integer

Start of the features to be used

0

-fend integer

End of the features to be used

0

-freverse Y/N

Reverse (if DNA)

N

C.2.4. Alignments

Table C.5. Alignment qualifiers
ACD datatypeQualifierDescriptionDefault value

Data type

Qualifier definition

Description

align

-aformat string

Alignment format

""

-aextension string

File name extension

""

-adirectory string

Output directory

""

-aname string

Base file name

""

-awidth integer

Alignment width

0

-aaccshow Y/N

Show accession number in the header

N

-adesshow Y/N

Show description in the header

N

-ausashow Y/N

Show the full USA in the alignment

N

-aglobal Y/N

Show the full sequence in alignment

N

C.2.5. Patterns

Table C.6. Pattern qualifiers
ACD datatypeQualifierDescriptionDefault value

pattern

-pformat string

File format

""

-pmismatch integer

Pattern mismatch

""

-pname string

Pattern base name

""

regexp

-pformat string

File format

""

-pname string

Pattern base name

""

C.2.6. Outputs

Table C.7. Output qualifiers.
ACD datatypeQualifierDescriptionDefault value

align

-aformat string

Alignment format

""

-aextension string

File name extension

""

-adirectory string

Output directory

""

-aname string

Base file name

""

-awidth integer

Alignment width

0

-aaccshow Y/N

Show accession number in the header

N

-adesshow Y/N

Show description in the header

N

-ausashow Y/N

Show the full USA in the alignment

N

-aglobal Y/N

Show the full sequence in alignment

N

featout

-offormat string

Output feature format

""

-ofopenfile string

Features file name

""

-ofextension string

File name extension

""

-ofdirectory string

Output directory

""

-ofname string

Base file name

""

-ofsingle Y/N

Separate file for each entry

N

outcodon

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

outdata

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

outdiscrete

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

outfile

-odirectory string

Output directory

""

outfileall

-odirectory string

Output directory

""

outfreq

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

outmatrix

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

outmatrixf

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

outproperties

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

outscop

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

outtree

-odirectory string

Output directory

""

-oformat string

Output format specific to this data type

""

report

-rformat string

Report format

""

-rname string

Base file name

""

-rextension string

File name extension

""

-rdirectory string

Output directory

""

-raccshow Y/N

Show accession number in the report

N

-rdesshow Y/N

Show description in the report

N

-rscoreshow Y/N

Show the score in the report

Y

-rusashow Y/N

Show the full USA in the report

N

-rmaxall integer

Maximum total hits to report

0

-rmaxseq integer

Maximum total hits to report for any one sequence

0

seqout

-osformat string

Output seq format

""

-osextension string

File name extension

""

-osname string

Base file name

""

-osdirectory string

Output directory

""

-osdbname string

Database name to add

""

-ossingle Y/N

Separate file for each entry

N

-oufo string

UFO features

""

-offormat string

Features format

""

-ofname string

Features file name

""

-ofdirectory string

Output directory

""

seqoutall

-osformat string

Output seq format

""

-osextension string

File name extension

""

-osname string

Base file name

""

-osdirectory string

Output directory

""

-osdbname string

Database name to add

""

-ossingle Y/N

Separate file for each entry

N

-oufo string

UFO features

""

-offormat string

Features format

""

-ofname string

Features file name

""

-ofdirectory string

Output directory

""

seqoutset

-osformat string

Output seq format

""

-osextension string

File name extension

""

-osname string

Base file name

""

-osdirectory string

Output directory

""

-osdbname string

Database name to add

""

-ossingle Y/N

Separate file for each entry

N

-oufo string

UFO features

""

-offormat string

Features format

""

-ofname string

Features file name

""

-ofdirectory string

Output directory

""

C.2.7. Reports

Table C.8. Report Qualifiers
ACD datatypeQualifierDescriptionDefault value

report

-rformat string

Report format

""

-rname string

Base file name

""

-rextension string

File name extension

""

-rdirectory string

Output directory

""

-raccshow Y/N

Show accession number in the report

N

-rdesshow Y/N

Show description in the report

N

-rscoreshow Y/N

Show the score in the report

Y

-rstrandshow Y/N

Show the nucleotide strand in the report

N

-rusashow Y/N

Show the full USA in the report

N

-rmaxall integer

Maximum total hits to report

0

-rmaxseq integer

Maximum total hits to report for any one sequence

0

C.2.8. Graphics

Table C.9. Graph qualifiers.
ACD datatypeQualifierDescriptionDefault value

graph

-gprompt Y/N

Graph prompting

N

-gdesc string

Graph description

""

-gtitle string

Graph title

""

-gsubtitle string

Graph subtitle

""

-gxtitle string

Graph x axis title

""

-gytitle string

Graph y axis title

""

-goutfile string

Output file for non interactive displays

""

-gdirectory string

Output directory

""

xygraph

-gprompt Y/N

Graph prompting

N

-gdesc string

Graph description

""

-gtitle string

Graph title

""

-gsubtitle string

Graph subtitle

""

-gxtitle string

Graph x axis title

""

-gytitle string

Graph y axis title

""

-goutfile string

Output file for non interactive displays

""

-gdirectory string

Output directory

""