A brief introduction to SEQtools 8.2 a comprehensive software suite for sequence handling and analysis.

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