Experiment file format                   Simon Dear, 15 February 1993
---------------------------------------------------------------------

The experiment file will contain every piece of information that will
ever needed to be known for the initial sequence processing, assembly,
oligo primer selection and automated walking.  This does not mean that
all records in the file will be stored in the new style database, as
many are clearly not relevant after the preprocessing stages.


Records in file
---------------

The order of records in the file is not important. They are listed
here in alphabetical order:

CC   (comment line)
CF   (Cloning vector sequence File)
CN   (Clone Name)
CS   (Cloning vector Sequence present in sequence)
CV   (Cloning Vector type)
DR   (Direction of Read)
DT   (DaTe of experiment)
EN   (Experiment Name)
EX   (EXperimental notes)
FM   (sequencing vector Fragmentation Method)
ID   (IDentifier)
LN   (Local format trace file Name)
LT   (Local format trace file Type)
MC   (MaChine on which experiment ran)
MN   (Machine generated trace file Name)
MT   (Machine generated trace file Type)
OP   (OPerator)
PN   (Primer Name)
PS   (Processing Status)
QL   (poor Quality sequence present at Left (5') end)
QR   (poor Quality sequence present at Right (3') end)
SC   (Sequencing vector Cloning site)
SF   (Sequencing vector sequence File)
SI   (Sequencing vector Insertion length)
SL   (Sequencing vector sequence present at Left (5') end)
SP   (Sequencing vector Primer site (relative to cloning site))
SQ   (SeQuence)
SR   (Sequencing vector sequence present at Right (3') end)
SS   (Screening Sequencing)
ST   (STrands)
SV   (Sequencing Vector type)
TN   (Template Name)


Explanation of records
----------------------

Record: CC   (comment line)
Format:	CC   string
Explanation:
A general comment line
be used by vep.

Record: CF   (Cloning vector sequence File)
Format:	CF   string
Explanation:
The name of the file containing the sequence of the cloning vector, to
be used by vep.

Record: CN   (Clone Name)
Format:	CN   string
Explanation:
The name of the physical map clone. The new database will allow
assembly of sequences from overlapping clones. Knowing the clone name
provides gap with mapping information about the sequence.

Record: CS   (Cloning vector Sequence present in sequence)
Format:	CS   range
Explanation:
Regions of sequence considered to be cloning vector. Used in assembly
to exclude unwanted sequence.

Record: CV   (Cloning Vector type)
Format:	CV   string
Explanation:
The type of the cloning vector used. Required for vep

Record: DR   (Direction of Read)
Format:	DR   direction
Explanation:
Which of forward or reverse primers were used. Useful for oligo primer
selection, and automated walking. Allows mapping of forward and
reverse reads off same template.

Record: DT   (DaTe of experiment)
Format:	DT   dd-mon-yyyy
Explanation:
The date on which the experiment file was created. Not used anywhere.

Record: EN   (Experiment Name)
Format:	EN   string
Explanation:
The name given to the experiment. Allows disassociation of the name of
the experiment file and the name that gets used by gap.

Record: EX   (EXperimental notes)
Format:	EX   string
Explanation:
Free format comment for additional information. Not used anywhere.

Record: FM   (sequencing vector Fragmentation Method)
Format:	FM   string
Explanation:
Fragmentation method used to create subclone (sequencing vector)
library. Non used anywhere.

Record: ID   (IDentifier)
Format:	ID   string
Explanation:
Same as EN (Experiment Name). This field is to make the experiment
file look like it is in EMBL format.

Record: LN   (Local format trace file Name)
Format:	LN   string
Explanation:
The name of the local format trace file. This information is passed
onto gap, and allows for local formats to be used.

Record: LT   (Local format trace file Type)
Format:	LT   string
Explanation:
The type of the local trace file type.

Record: MC   (MaChine on which experiment ran)
Format:	MC   string
Explanation:
The lab's name for the sequencing machine used to create the data. Is
this useful?

Record: MN   (Machine generated trace file Name)
Format:	MN   string
Explanation:
The name of the trace file generated by the sequencing machine MC.

Record: MT   (Machine generated trace file Type)
Format:	MT   string
Explanation:
The type of MN.

Record: OP   (OPerator)
Format:	OP   string
Explanation:
Someone's name, possibly the person who ran the script. Not used anywhere.

Record: PN   (Primer Name)
Format:	PN   string
Explanation:
Name of primer used, using local naming convention. Could be a
universal primer. May be useful one day. Not used currently.

Record: PS   (Processing Status)
Format:	PS   explanation
Explanation:
Indication of processing status. The presence of this entry indicates
failure of some kind, and the experiment file should not be further
processed.

Record: QL   (poor Quality sequence present at Left (5') end)
Format:	QL   position
Explanation:
The sequence up to and including the base at the marked position are
considered too poor quality to be considered. May overlap with other
marked sequences - CS, SL or SR. Used in assembly to exclude unwanted
sequence.

Record: QR   (poor Quality sequence present at Right (3') end)
Format:	QR   position
Explanation:
The sequence from and including the base at the marked position to the
end are considered too poor quality to be considered. May overlap with
other marked sequences - CS, SL or SR. Used in assembly to exclude
unwanted sequence.

Record: SC   (Sequencing vector Cloning site)
Format:	SC   position
Explanation:
The cloning site of the sequence vector, based on local knowledge of
the sequence vector. Used by vep.

Record: SF   (Sequencing vector sequence File)
Format:	SF   string
Explanation:
The name of the file containing the sequence of the sequencing vector,
to be used by vep.

Record: SI   (Sequencing vector Insertion length)
Format:	SI   range
Explanation:
Suspected insertion length of subclone. Useful for selecting templates
in oligo primer selection.

Record: SL   (Sequencing vector sequence present at Left (5') end)
Format:	SL   position
Explanation:
The sequence up to and including the base at the marked position are
considered to be sequencing vector. Used in assembly to exclude
unwanted sequence.

Record: SP   (Sequencing vector Primer site (relative to cloning site))
Format:	SP   position
Explanation:
Location of the primer using to sequence relative to cloning site.
Used by vep.

Record: SQ   (SeQuence)
Format:	SQ   \nsequence...\n\\\n
Explanation:
Complete sequence, as determined by the sequencing machine.

Record: SR   (Sequencing vector sequence present at Right (3') end)
Format:	SR   position
Explanation:
The sequence from and including the base at the marked position to the
end are considered to be sequencing vector. Used in assembly to
exclude unwanted sequence.

Record: SS   (Screening Sequencing)
Format:	SS   string
Explanation:
Sequences to screen sequence against. To screen against more that one
sequence, it is permissible to include more that one SS line. The
field is used by the script screen-against-vector from within squirrel.
Experiments partially matching a screen file will have a PS line added
to the end.

Record: ST   (STrands)
Format:	ST   number
Explanation:
Indicating whether this is a single or double stranded template. This
is useful in oligo primer selection, for deducing suitable templates.

Record: SV   (Sequencing Vector type)
Format:	SV   string
Explanation:
Name of sequencing vector used in experiment. Allows preference lists
to be set up for choosing templates in selecting oligos.

Record: TN   (Template Name)
Format:	TN   string
Explanation:
The name of the template used in the experiment.



Example File
------------

The information so far included here is easily derivable from the
trace file, using various scripts and a few look-up tables. This
example is based on one created automatically:


ID   h4a01h6.s1
EN   h4a01h6.s1
TN   h4a01h6
EX   lane 18, run time 10 hrs
MN   Sample 18
MC   A
MT   ABI
LN   h4a01h6.s1SCF
LT   SCF
DT   08-Jan-1993
CC   Dir: /home/sd/Mac-files-sd/Results F 16_12_92.2
OP   sd
TN   h4a01h6
SV   M13mp18
SF   /home/sd/squirrel/seqs/m13mp18.vec
SI   1000..2000
SC   6249
FM   shear
PN   -21
DR   +
SP   41
ST   1
CN   3G9
CV   sCos-1
CF   /home/sd/squirrel/seqs/sCos-1.seq
SS   /home/sd/squirrel/seqs/Alu.seqs
SS   /home/sd/squirrel/seqs/schrrIII.seq
SQ
     GCTTGCATGC CTGCAGGTCG ACTCTAGAGG ATCCCCAACC AGTAAGGCAA CCCCGCCAGC
     CTAGCCGGGT CCTCAACGAC AGGAGCACGA TCATGCGCAC CCGTCAGATC CAGACATGAT
     AAGATACATT GATGAGTTTG GACAAACCAC AACTAGAATG CAGT-AAAAA AATGCTTTAT
     TTGTGAAATT TGTGATGCTA TTGCTTTATT TGTAACCATT ATAAGCTGCA ATAAACAAGT
     TAACAACAAC AATTGCATTC ATTTTATGTT TCAGGTTCAG GGGGAGGTGT GGGAGGTTTT
     TTAAAGCAAG TAAAACCTCT ACAAATGTGG TATGGCTGAT TATGATCTCT AGTCAAGGCA
     CTATACATCA AATATT-CCT TATTAACCCC CTTTACAAAT TTAAAAGGCT -AAAGGGTCC
     ACAATTTTTG -GCCTAGGTA TTAATAGCCG GCACTTCTT- TGCCTGTTTT GG-GTAGGG-
     AAAACCGGTA TGTTT-TGGT T-TTC
//
CC   Quality clipping by newted May-1992
QL   0
QR   281
SL   36
SR   506
CS   37..280
PS   Completely cloning vector
