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

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Presentation on theme: "A brief introduction to SEQtools 8.2 a comprehensive software suite for sequence handling and analysis."— Presentation transcript:

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

2 what’s behind the SEQtools menus ? an overview of seqtools functions and facilities

3 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 3 start form

4 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 4 short file menu

5 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 5 main editor

6 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 6 long file menu

7 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 7 edit menu

8 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 8 translate menu

9 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 9 search menu

10 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 10 retrieve menu

11 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 11 compare menu

12 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 12 analyse menu

13 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 13 header menu

14 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 14 project menu

15 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 15 launch menu

16 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 16 tools menu

17 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 17 special menu

18 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 18 www menu

19 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 19 preferences menu

20 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 20 help menu

21 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

22 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

23 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

24 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

25 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

26 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

27 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

28 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)

29 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

30 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

31 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

32 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 32 header structure, 3-D array

33 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

34 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

35 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 35 description lines cont...

36 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

37 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

38 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

39 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

40 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

41 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

42 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

43 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

44 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

45 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 45 aligning step 1 display sorted sequences list... highlight genes to align...

46 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 46 aligning step 2 run ClustalW with selected sequences...

47 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 47 aligning step 3 look at the alignment, is it nice and correct ?

48 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

49 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)

50 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

51 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

52 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

53 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

54 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

55 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

56 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

57 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

58 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

59 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

60 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

61 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 61 file tools

62 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

63 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

64 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

65 Clustal w alignment: upper line: MegaBACE lower line: LifeTrace ?

66 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 66 user interface to trace file processing

67 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 67 LifeTrace quality data

68 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 68 removal of vector sequence

69 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

70 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 70 SAGE – file manipulation

71 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 71 SAGE – expression analysis

72 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 72 SAGE - expression analysis

73 Copyright S.W. Rasmussen 1995 – 2004, all rights reserved Slide 73 microarray design functions... microtiter plate indexing utility microarray layout utility special functions - microarray

74 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

75 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 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


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