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A brief introduction to
SEQtools 8.2
a comprehensive software suite for sequence handling and analysis
what’s behind the SEQtools menus ?
an overview of seqtools functions and facilities
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 3
start form
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 4
short file menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 5
main editor
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 6
long file menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 7
edit menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 8
translate menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 9
search menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 10
retrieve menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 11
compare menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 12
analyse menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 13
header menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 14
project menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 15
launch menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 16
tools menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 17
special menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 18
www menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 19
preferences menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 20
help menu
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 21
overview
seqtools...
• is a stand-alone program suite
• is a true ”multi-sequence” application
• uses a virtual ”pseudo” database
• includes batch functions for multi-sequence analysis
• contains a large collection of "utilities"
• has a flexible program (code) structure
• offers routines on-demand to meet your requirements
• can be used free of charge
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 22
history
seqtools...
• started in 1995 as ”Rename” to change file names of sequence files generated by a ABI 373-sequencer
• developed mainly driven by frustration with early versions of commercial software packages
• expanded during the yeast genome sequencing project
• while performing SAGE and microarray analyses of gene expression
• and not least as the result of the feedback from some 1,000 users worldwide since 1998
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 23
brief descriptions
a guided tour...
• projects and subprojects
• headers and description lines
• trivial functions
• automated functions
• utilities
• special functions
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 24
what is a project ?
a project is…
• a collection of 1 to 99,999 sequences
• including either
• nucleotide sequences
• or amino acid sequences
• or primer sequences
• or chromatograms
• stored in a ”pseudo-database” in RAM
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 25
how do I create a project ?
projects are created…
• by loading
• sequence files
• multi-sequence files
• chromatograms
• project files
• or by entering sequences manually
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 26
can I modify a project ?
projects can be modified by…
• adding more sequences to the project
• removing sequences from the project
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 27
what are subprojects ?
additional instances of SEQtools…
• groups of sequences included in a project can be isolated and opened as a new project in a separate instance of SEQtools
• each instance of SEQtools has its own set of preferences and auto-backup folder
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 28
how are projects saved ?
projects can be saved as…
• separate, single sequences
• a single multi-sequence file (flat-file)
• a compressed multi-sequence file
• a project file *.psg (file-path list)
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 29
sequence file formats
supported sequence formats…
• default: special SEQtools sequence format
• default: special SEQtools primer format
• imports most common sequence formats
• exports in several formats
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 30
brief descriptions
a guided tour…
• projects and subprojects
• headers and description lines
• trivial functions
• automated functions
• utilities
• special functions
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 31
header structure…
• 3D array storing search results, user comments etc. for each sequence
• the amount of information is only limited by the available memory
• the displayed header may include all or user selected parts of the information stored in the sequence header
• the displayed headers are searchable
• database search results stored in headers can be automatically updated
sequence annotation
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 32
header structure, 3-D array
M DB search resu ltsS ubS ec t ion Index = 4
F astA Defin itionS ubS ec t ion Index = 3
Descrip tio n lineS ubS ec t ion Index = 2
User Co m m en tsS ubS ec t ion Index = 1
GENERALS ec t ion Index = 0
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTNS ec t ion Index = 1
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTXS ec t ion Index = 2
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTPS ec t ion Index = 3
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
TBLASTNS ec t ion Index = 4
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
TBLASTXS ec t ion Index = 5
Co n sen su s seqS ubS ec t ion Index = 4
SAG E d ataS ubS ec t ion Index = 3
2-seq co m p areS ubS ec t ion Index = 2
Im p o rted an n o tationS ubS ec t ion Index = 1
SPECIALS ec t ion Index = 6
H e a d er M a inH eade rIndex = 1
Header Array StructureSeq(N).H(Sec tionIndex, Sub SectionIndex, HeaderIndex )
R eD im S eq .H (0 to 6 , 1 to 4 , 1 to n)
M DB search resu ltsS ubS ec t ion Index = 4
F astA Defin itionS ubS ec t ion Index = 3
Descrip tio n lineS ubS ec t ion Index = 2
User Co m m en tsS ubS ec t ion Index = 1
GENERALS ec t ion Index = 0
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTNS ec t ion Index = 1
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTXS ec t ion Index = 2
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTPS ec t ion Index = 3
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
TBLASTNS ec t ion Index = 4
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
TBLASTXS ec t ion Index = 5
Co n sen su s seqS ubS ec t ion Index = 4
SAG E d ataS ubS ec t ion Index = 3
2-seq co m p areS ubS ec t ion Index = 2
Im p o rted an n o tationS ubS ec t ion Index = 1
SPECIALS ec t ion Index = 6
H e a d er M a inH eade rIndex = 1
Header Array StructureSeq(N).H(Sec tionIndex, Sub SectionIndex, HeaderIndex )
R eD im S eq .H (0 to 6 , 1 to 4 , 1 to n)
M DB search resu ltsS ubS ec t ion Index = 4
F astA Defin itionS ubS ec t ion Index = 3
Descrip tio n lineS ubS ec t ion Index = 2
User Co m m en tsS ubS ec t ion Index = 1
GENERALS ec t ion Index = 0
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTNS ec t ion Index = 1
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTXS ec t ion Index = 2
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTPS ec t ion Index = 3
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
TBLASTNS ec t ion Index = 4
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
TBLASTXS ec t ion Index = 5
Co n sen su s seqS ubS ec t ion Index = 4
SAG E d ataS ubS ec t ion Index = 3
2-seq co m p areS ubS ec t ion Index = 2
Im p o rted an n o tationS ubS ec t ion Index = 1
SPECIALS ec t ion Index = 6
H e a d er M a inH eade rIndex = 1
Header Array StructureSeq(N).H(Sec tionIndex, Sub SectionIndex, HeaderIndex )
R eD im S eq .H (0 to 6 , 1 to 4 , 1 to n)
M DB search resu ltsS u bS e c t ion In d e x = 4
F astA Defin itionS u bS e c t ion In d e x = 3
Descrip tio n lineS u bS e c t ion In d e x = 2
User Co m m en tsS u bS e c t ion In d e x = 1
G ENERALS e c t io n Ind e x = 0
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLAST NS e c t io n Ind e x = 1
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLASTXS e c t io n Ind e x = 2
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLASTPS e c t io n Ind e x = 3
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
TBLAST NS e c t io n Ind e x = 4
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
TBLAST XS e c t io n Ind e x = 5
Co n sen su s seqS u bS e c t ion In d e x = 4
SAG E d ataS u bS e c t ion In d e x = 3
2-seq co m p areS u bS e c t ion In d e x = 2
Im p o rted an n o tationS u bS e c t ion In d e x = 1
SPECIALS e c t io n Ind e x = 6
H e a d er M a inH ea d e rIn d e x = 1
Header Array StructureSeq(N).H(Sec tionIndex, Sub SectionIndex, HeaderIndex )
R eD im S eq .H (0 to 6 , 1 to 4 , 1 to n)
M DB search resu ltsS u bS e c t ion In d e x = 4
F astA Defin itionS u bS e c t ion In d e x = 3
Descrip tio n lineS u bS e c t ion In d e x = 2
User Co m m en tsS u bS e c t ion In d e x = 1
G ENERALS e c t io n Ind e x = 0
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLAST NS e c t io n Ind e x = 1
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLASTXS e c t io n Ind e x = 2
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLASTPS e c t io n Ind e x = 3
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
TBLAST NS e c t io n Ind e x = 4
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
TBLAST XS e c t io n Ind e x = 5
Co n sen su s seqS u bS e c t ion In d e x = 4
SAG E d ataS u bS e c t ion In d e x = 3
2-seq co m p areS u bS e c t ion In d e x = 2
Im p o rted an n o tationS u bS e c t ion In d e x = 1
SPECIALS e c t io n Ind e x = 6
H e a d er M a inH ea d e rIn d e x = 1
Header Array StructureSeq(N).H(Sec tionIndex, Sub SectionIndex, HeaderIndex )
R eD im S eq .H (0 to 6 , 1 to 4 , 1 to n)
M DB search resu ltsS ubS ec t ion Index = 4
F astA Defin itionS ubS ec t ion Index = 3
Descrip tio n lineS ubS ec t ion Index = 2
User Co m m en tsS ubS ec t ion Index = 1
GENERALS ec t ion Index = 0
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTNS ec t ion Index = 1
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTXS ec t ion Index = 2
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
BLASTPS ec t ion Index = 3
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
TBLASTNS ec t ion Index = 4
M ed L ineS ubS ec t ion Index = 4
Su b m issionS ubS ec t ion Index = 3
Alig n m entS ubS ec t ion Index = 2
Descrip tio nS ubS ec t ion Index = 1
TBLASTXS ec t ion Index = 5
Co n sen su s seqS ubS ec t ion Index = 4
SAG E d ataS ubS ec t ion Index = 3
2-seq co m p areS ubS ec t ion Index = 2
Im p o rted an n o tationS ubS ec t ion Index = 1
SPECIALS ec t ion Index = 6
H e a d er M a inH eade rIndex = 1
Header Array StructureSeq(N).H(Sec tionIndex, Sub SectionIndex, HeaderIndex )
R eD im S eq .H (0 to 6 , 1 to 4 , 1 to n)
M DB search resu ltsS u bS e c t ion In d e x = 4
F astA Defin itionS u bS e c t ion In d e x = 3
Descrip tio n lineS u bS e c t ion In d e x = 2
User Co m m en tsS u bS e c t ion In d e x = 1
G ENERALS e c t io n Ind e x = 0
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLAST NS e c t io n Ind e x = 1
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLASTXS e c t io n Ind e x = 2
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
BLASTPS e c t io n Ind e x = 3
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
TBLAST NS e c t io n Ind e x = 4
M ed L ineS u bS e c t ion In d e x = 4
Su b m issionS u bS e c t ion In d e x = 3
Alig n m entS u bS e c t ion In d e x = 2
Descrip tio nS u bS e c t ion In d e x = 1
TBLAST XS e c t io n Ind e x = 5
Co n sen su s seqS u bS e c t ion In d e x = 4
SAG E d ataS u bS e c t ion In d e x = 3
2-seq co m p areS u bS e c t ion In d e x = 2
Im p o rted an n o tationS u bS e c t ion In d e x = 1
SPECIALS e c t io n Ind e x = 6
H e a d er M a inH ea d e rIn d e x = 1
Header Array StructureSeq(N).H(Sec tionIndex, Sub SectionIndex, HeaderIndex )
R eD im S eq .H (0 to 6 , 1 to 4 , 1 to n)
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 33
the displayed headers may include…
• results of several database searches
• entrez records (sequence and/or medline)
• multi-sequence alignments
• user comments
• default section / all sections
• results from various separate analyses
the displayed header
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 34
sequence description lines
default description lines...
• best match from selected (default) blast section
• used in sequence listing throughout the program
• extensive facilities for formatting descriptions
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 35
description lines cont...
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 36
data safety
data safety...
• ten-step undo function
• automated timed backup function
• original sequence files are not permanently affected by editorial changes before the project is saved
• sequence checksums to verify sequence integrity
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 37
brief descriptions
a guided tour…
• projects and subprojects
• headers and description lines
• trivial functions
• automated functions
• utilities
• special functions
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 38
trivial functions
some trivial DNA functions...
• sequence editing
• nucleotide-to-protein translation
• restriction enzyme mapping
• codon usage analysis
• database searching
• sequence alignment
• sequence comparison
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 39
editing
editing sequences and file names...
• user defined color patterns
• upper case / lower case / both
• sequence numbering (offset, reverting)
• sequence convertion: watson / crick / inverted
• project sequence names
• sequence file names
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 40
translation
translation options
• translate in specified reading frame
• find longest ORF/fragment in all frames
• display map, three forward frames
• create and store protein files
• back-translate nucleotide sequences
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 41
restriction maps
restriction enzyme mapping
• downloading and converting enzyme data files
• building enzyme groups
• display options: list or map
• plasmid editor
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 42
codon usage
codon usage analysis...
• reading *.cod files
• creating a *.cut file
• preferred codons / avoided codons
• degeneration level
• back-translation
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 43
comparing
comparing two sequences...
• sequences, general
• dot blot
• blast two-sequences
• blast one sequence against rest of project
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 44
aligning
third party programs...
• clustal w, standard alignment program, seqtools interface
• clustal x, standard alignment program with user interface
• genedoc, advanced alignment editor
• t-coffee, advanced alignment optimisation
• seqtools contig builder
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 45
aligning step 1
display sorted sequences list...
highlight genes to align...
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 46
aligning step 2
run ClustalW with selected sequences...
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 47
aligning step 3
look at the alignment, is it nice and correct ?
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 48
aligning step 4
if not - auto-transfer alignment to GeneDoc for further editing or even better run t-coffee optimisation
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 49
searching
find...
• in current sequence
• in project
• in headers
• similar sequences (clustering)
• repeats in sequence
• potential introns (GT - AG regions)
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 50
protein functions
special protein facilities...
• protein properties
• hydropathy plot
• dot plot with protein replacement scheme
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 51
brief descriptions
a guided tour…
• projects and subprojects
• headers and description lines
• trivial functions
• automated functions
• utilities
• special functions
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 52
automated functions - blast
batch search and annotation...
• blast searching
• on in-house blast servers
• as client at NCBI
• local blast, single database
• local blast, multiple databases
• entrez, information retrieval
• automated sequence annotation
• entrez standard user interface
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 53
automated functions - parsing
parsing search results into headers...
• blast description lines
• blast alignments
• original submitted sequence
• medline record from Entrez
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 54
automated functions - MDB search
local multi-database search...
• search all sequences in project
• against multiple local databases
• process search result
• store search result in header
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 55
brief descriptions
a guided tour…
• projects and subprojects
• headers and description lines
• trivial functions
• automated functions
• utilities
• special functions
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 56
utilities - translators, calculators
general facilities...
• IUB symbols
• codon to amino acids - and back
• mathematic calculator
• dna concentration calculator
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 57
utilities - data files
search data files...
• convert a project into a search data file
• convert GCG restriction enzyme file from ReBase
• search data file editor
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 58
utilities - multi-sequence operations
with these functions you can....
• build flatfiles
• build fasta ms files
• break-up ms files into single sequences
• trim sequence annotation
• fasta definition line editor
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 59
utilities - local databases
create local databases from....
• sequences in project
• sequence files on disk
• fasta definition line editor
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 60
utilities - file tools
batch processing files...
• view / find in sequence files
• view LifeTrace data files
• file and folder tools
• create EST submission files for GenBank
• batch create 6-frame translations of dna sequences
• view / decode primer orders
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 61
file tools
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 62
primer projects
facilities for primer design...
• typing / editing
• back-translation
• primer properties
• convert to search datafile
• primer ordering by e-mail
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 63
brief descriptions
a guided tour…
• projects and subprojects
• headers and description lines
• trivial functions
• automated functions
• utilities
• special functions
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 64
basecalling with LifeTrace...
• advanced routine for basecalling trace files
• and auto-trimming raw sequence files
• removal of vector from raw sequence files
special functions - basecalling
Clustal w alignment:
upper line: MegaBACElower line: LifeTrace
?
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 66
user interface to trace file processing
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 67
LifeTrace quality data
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 68
removal of vector sequence
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 69
serial analysis of gene expression...
• extraction and processing of sage tags
• sage-profile handling
• sage-mapping file from EST data
• expression analysis
special functions - SAGE analysis
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 70
SAGE – file manipulation
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 71
SAGE – expression analysis
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 72
SAGE - expression analysis
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 73
microarray design functions...
• microtiter plate indexing utility
• microarray layout utility
special functions - microarray
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 74
how to get help ?
getting help...
• context sensitive help
• how to...
• web based manual
• ask me at [email protected]
Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 75
how to get the program?
download and install...
1. visit the seqtools homepage at www.seqtools.dk
2. navigate to the download page and get the installation file
3. install seqtools 8.2 on your PC
4. start seqtools and goto ”help/seqtools configuration”
5. install auxiliary programs from the configuration form
6. install emboss programs from the configuration form
7. register your copy of seqtools
