CSC

Records

It is important to note that the assembly program gap4 (see section Gap4 introduction) will not operate to its full effect if it is not given all the necessary data. For example gap4 contains many functions that can analyse the positions and relative orientations of readings from the same template in order to check the correctness of the assembly and determine the contig order. However if the records that name templates and their estimated lengths, and define the primers used to obtain readings from them are missing, none of these valuable analyses can be performed reliably. One way to ensure that all the necessary fields are present is to use the program pregap4 (see section Pregap4 introduction).

In the descriptions below records containing * are those read into the database during normal assembly; those with ** are extra items required when entering pre-assembled data; those with *** are read from SCF files (after the experiment file has been read to obtain the SCF file name); (see section SCF introduction) the record marked **** is an extra item required for Directed Assembly.

The order of records in the file is not important. They are listed here in alphabetical order with, where possible, reasons for the origin of their names. Several are redundant and no group is likely to make use of them all. Obviously others can be added in the future. Initially they might be of local use but if their use becomes wider they can be added to the standard set. Standard EMBL records such as FT are assumed to be included.

AC

ACcession number

AP

Assembly Position ****

AQ

AVerage Quality for bases 100..200

AV

Accuracy values for externally assembled data **, ***

BC

Base Calling software

CC

Comment line

CF

Cloning vector sequence File

CH

Special CHemistry

CL

Cloning vector Left end

CN

Clone Name

CR

Cloning vector Right end

CS

Cloning vector Sequence present in sequence *

CV

Cloning Vector type

DR

Direction of Read

DT

DaTe of experiment

EN

Entry Name

EX

EXperimental notes

FM

sequencing vector Fragmentation Method

ID

IDentifier *

LE

was Library Entry, but now identifies a well in a micro titre dish

LI

was subclone LIbrary but now identifies a micro titre dish

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

ON

Original base Numbers (positions) **

OP

OPerator

PC

Position in Contig **

PD

Primer data (the sequence of a primer)

PN

Primer Name

PR

PRimer type *

PS

Processing Status

QL

poor Quality sequence present at Left (5') end *

QR

poor Quality sequence present at Right (3') end *

RS

Reference Sequence for numbering and mutation detection

SC

Sequencing vector Cloning site

SE

SEnse (ie whether complemented) **

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 Sequence

ST

STrands *

SV

Sequencing Vector type *

TG

Gel reading Tag *

TC

Contig Tag *

TN

Template Name *

WT

Wild type trace