Applied Biosystems

Sequence Scanner Software v1.0

September 2005



These release notes contain the most current set of information about Sequence Scanner Software v1.0.
Please review these notes prior to installing the application.

Table of Contents:

A. Introduction to Sequence Scanner Software v1.0
B. Features in Sequence Scanner Software v1.0
C. Compatible Operating Sstems and !inimum Sstems "equirements
#. Installing Sequence Scanner Software v1.0
$. %nown Issues

A. Introuction to Sequence Scanner Software v1.0
Sequence Scanner Software v1.0 allows users to view! print an e"port sequencing sample files generate
using Applie #ios$stems genetic anal$%er instruments. This software will also enable users to eit bases!
manuall$ trim a sequence rea an generate reports. #ase calling an auto&trimming features are not
supporte in Sequence Scanner Software.

This software reas .ab1 files generate from A#I P'IS( )10! )**! )*00 +,A Anal$%er an Applie
#ios$stems )100&Avant! )100! )1)0-)1)0"l an )*)0-)*)0"l s$stems.

B. Features in Sequence Scanner Software v1.0
Import Traces
& Traces can be importe via rag an rop! ouble clic.ing on file an the /Import Traces/
ialog.

+ispla$ Traces
& Traces liste in a tabular format with several ispla$ categories.
& Traces can be viewe as thumbnails.
o Thumbnails ispla$ raw ata an can be scale uniforml$ or
iniviuall$.
& Traces can be sorte b$ a variet$ of categories within both the tabular or thumbnail formats.
& Traces can be viewe iniviuall$ or as a group.
o (ultiple traces can be ispla$e b$ tiling iniviual trace viewers in
0"0! )"1! 0"1 an 1"0 moes.
& Anal$%e an raw ata can be ispla$e simultaneousl$ with the abilit$ to nuge the raw ata
in either irection to align with the anal$%e ata.
& +$namic %ooming b$ ragging the mouse over a range of interest.

1"port Traces
& Traces can be e"porte in .t"t! .seq! .scf! 2peg! pf! .qual! .fsta an .ph.1 file formats.
& Traces can be e"porte with onl$ the post&trim sequence information to .seq! .fsta an .qual
files.

Print Traces
& Print preview capabilit$ for traces
& Printing of the anal$%e! annotation an sequence views within traces
& Configurable trace printout settings

1it Traces
& 1it! elete! insert bases with uno an reo support
& A or remove bases to be inclue in the post&trim sequence

'eport 'esults
& Sequence Scanner provies seven reports for the importe trace files: 3ualit$ Control! Plate!
Trace Score! C'4 5Continuous 'ea 4ength6! C'4 +istribution! 37008! an Signal Strength.
& +ata points within the reports are h$perlin.e bac. to the trace files to open them in the trace
viewer
& 'eport settings are configurable
& Print previews are available for all reports
& 'eports can also be e"porte in .pf! .html! .t"t an ."ls formats.

9ser Preferences
& Configurable threshols for low! meium an high Trace Scores an Continuous 'ea 4ength
metrics
& Configurable color for 3ualit$ 7alues! Trace Scores an Continuous 'ea 4engths

(iscellaneous
& Import traces ialog will alwa$s map to the last&use foler location between sessions

C. Compatible Operating Sstems and !inimum Sstems "equirements
This software is compatible with :inows 0000 ;S sp< an :inows =P ;S sp0.
The minimum s$stem requirements are >10(# 'A(! *))(?% CP9! 1@# of har is. space. The
performance improves significantl$ with higher configuration computers.

#. Installing Sequence Scanner Software v1.0

1. +ownloa the installer from the web page b$ clic.ing on the lin. an then selecting /;pen/ or
/Save/ from the /Aile +ownloa/ ialog.
0. If $ou choose to save the installer to is.! then launch the installer b$ either selecting /;pen/ in
the /+ownloa complete/ ialog or ouble&clic.ing the ownloae SeqScannerInstall.e"e file
). Aollow the installation wi%arBs instructions to install Sequence Scanner v1.0.

$. %nown Issues
Installer
& It has been observe uner rare circumstances that an install of the Sequence Scanner
software following an uninstall will fail ue to an installation error.
o If $ou e"perience this problem! simpl$ restart $our computer an
repeat installation.

Printing
& :hen printing traces on the ?PC100 printer! the avance printing features must be enable
for printing of multiple traces to properl$ print out all of the selecte traces.
o To enable the avance printing features! open the /Properties/ ialog
for the printer b$ right&clic.ing on the ?PC100 printerBs icon within the
/Print/ ialog an selecting /properties/. Arom within the ialogBs
/Avance/ tab! chec. the /1nable avance printing features/
chec.bo".
& Incomplete printing 2ob ue to insufficient paper in the printing tra$ 5Printer ?P C1006
o ;n the ?PC100 printer! if a printing 2ob is interrupte ue to
insufficient paper! the printout ma$ ispla$ printing errors.
& 4ater annotation an sequence pages blan. uring a print 2ob with a large number 5D0006 of
traces 5Printer ?P C1006
o ;n the ?PC100 printer! it has been observe that the annotation an
sequence pages containe no ata for trace 00C an above when
printing <)0 trace files.

Importing Traces
& Import of traces fails for traces that have been eite in SeqA v).* to elete an then re&insert
a base. The result is that none the traces selecte for import are ispla$e in the /Trace
(anager/.
& In some instances! if importing of traces fails! Sequence Scanner will isallow subsequent
attempts to import an$ of the traces from the faile import.
o :or.aroun: 1"it an re&launch Sequence Scanner. 'epeat attempt to
import traces.

1"porting Traces
& :hen e"porting traces to 2pg or pf formats! software errors ma$ occur if available memor$
is low ue to running of other applications in the bac.groun.
o If $ou e"perience this problem! tr$ closing out of all other
applications prior to e"porting traces.
& If $ou attempt to e"port traces that have ientical trace file names! the last of these traces to
be e"porte will overwrite the previous ones. This is ue to the convention of naming the
e"port files base on the original trace file names.
o :or.aroun: To avoi this! simpl$ split the trace files with ientical
names into separate e"ports! specif$ing ifferent estination folers for
each e"port.

1iting #ases
& 1ite bases fail to convert bac. to uppercase when elete an then re&inserte with the
same base label.
o 1ite bases are ispla$e as lowercase to istinguish them from
calle bases. ,ormall$! when an eite base is change bac. to its
original call it is again ispla$e as uppercase as though it was never
eite. This behavior oes not hol true in the case of a base eletion
an then re&insertion.

'emove Traces
& If the remove traces operation is cancelle from the /Save changes to all trace files.../ ialog!
the operation then has no effect on subsequent attempts for the same selection of traces if
initiate from the file menu or toolbar.
o :or.aroun: 'eselect the traces for removal or select /'emove
Traces/ from the /Aile Tas.s/ menu.

Securit$ :arning
& ;n :inows =P! a securit$ warning ma$ be issue when launching Sequence Scanner if the
firewall is enable. :e recommen leaving the firewall enable but selecting 9nbloc. in the
ispla$e warning ialog.


A#I P'IS( an Applie #ios$stems are registere traemar.s of Applera Corporation or
its subsiiaries in the 9S an-or certain other countries.
A# 5+esign6! Applera an Celera +iscover$ S$stems are traemar.s of Applera Corporation or its
subsiiaries in the 9S an-or certain other countries.
All other traemar.s are the propert$ of their respective owners.
Cop$right 000> Applie #ios$stems. All rights reserve.
September 000>