questions and answers

SEQtools includes several hundred functions and routines not all equally well documented in the context sensitive help and the web manual. On this page I have collected some questions (?) and answers (!) in no particular order.

? How do I check if other sequences in my project are similar to the one I am current looking at? ! Simply press F5 to perform a local BlastN or BlastP search on all sequences contained in the project. Click the result list to retrieve a match and shift-click to align the similar sequences with ClustalW.

Remember to enter the correct parameters for the local blast function in project preferences.
? When I run several instances of SEQtools simultaneously it is difficult to identify which forms that belong to the same instance. ! You can color code individual instances of SEQtools, Preferences>Application Color Coding, to give each instance of SEQtools its own color.
? My project includes 2000 primer sequences. I wish to aliquot the primers in 96-well microtiter plates with defined positions left blank. ! Use the microtiter plate indexing function, Special>Microarray Tools, to print sheets with the primer names precisely matching the microtiter plate.

Place the plate over the template and read the primer names through the bottom of the plates. The template print function includes a utility to design the blank pattern.
? The filenames of my sequences are not very logical. It is possible to re-name sequence files. ! Yes. Seqtools has two functions for batch re-naming sequence files, Edit>Names>Edit Sequence Names. In addition it is possible to edit each filename separately.

As SEQtools can load many files (more than 15,000 short est sequences) careful validation of filenames takes place while loading to avoid duplicate filenames in the project
? I have performed a batch blast search on all the sequences in my project. The search, however, failed for a few sequences. Do I have to repeat the search for each of these separately. ! No. Open the sequence listing form, Sort the list according to description lines and highlight those with a "*No information" label. Open the ncbi blast form and find the Project settings tab. Check the checkbox to select the highlighted sequences. And start the blast search.
? I need tools to perform clustering of my EST sequences. ! SEQtools includes several clustering functions, Compare>Clustering. A 'quick and dirty' overview function and three yielding detailed information on the sequence clusters.
? I am planning a microarray based on 50-mer oligo nucleotides. Are there functions in SEQtools to assist me with this task. ! Yes. New functions have been added to create index files for microtiter plates as well as for creating microarray layout. Look under Special functions. The functions for microarray design are closely integrated with the blast database search functions.
? How do I customise SEQtools for my particular needs. ! SEQtools includes seven Preferences forms each containing a number of options allowing you to customise the program in a number of ways.
? Is it possible to export sequences from SEQtools in formats compatible with other programs. ! Yes, you can export sequences in Genbank, Vector NTI, FastA, LaserGene, GCG Wisconsin, EMBL and as plain text. For FastA formats SEQtools includes an advanced editor for composing the definition line, Tools>Editors>FastA Definition Line Editor.
? I have a list of accession numbers and would like to get the corresponding genbank GI numbers. ! Use the conversion function: Tools>Conversion Functions>Convert Genbank AC Numbers To GI List..."
? I wish to edit my restriction enzyme data file. Is this possible in SEQtools. ! Yes, SEQtools contains a separate editor which enables you to edit/add/remove individual entries in your enzyme data file, Tools>Editors>Search Data File Editor. It is possible to compose a sub enzyme data file containing only enzymes with selected characteristics such as: producing 5' overhangs, 3' overhangs, palindromic enzymes etc. Finally you can convert sequences contained in a SEQtools project into a sear data file.
? My project contains 400 human GPCR protein sequences and I would like to retrieve rat orthologs for the same genes. ! Perform a batch BlastP search at NCBI on the nr database with the "rat" limiter. Use the Retrieve>New Project From Blast Results... function to create a new project including rat orthologs identified by the blastp search.
? When I click "L" to display the sequence list and choose the view option "Description Line" the "Description" column is empty. ! This is either because no blast results are available for the sequences - or because you have not composed a "Virtual Blast Section".
? In the sequence list the rows are not sorted correctly when I click the "Expect" column. ! The form used to display the list is unable to sort numerical values. Sorry...
? How do I perform a batch blast search at NCBI. ! Simply load the sequences you wish to search into a project. Then open the Search>Blast Batch Search select the method and set the necessary parameters and cstart the search. The search results are collected in the sequence headers.
? I have very large sequence headers. How do I customise the displayed headers. ! Open the "Compose Header" form by right-clicking the text header icon (an open book) and choose which sections you wish to include in the displayed header.
? I need to construct a fasta multi-sequence file and want to include specific items from the sequence annotation in the definition line. ! Use the fasta definition line editor Tools>Editors to compose the definition line.
? I wish to convert a downloaded Locus Link search for "rattus map protein kinases" into a systematically organised file containing only certain items from the original list.  ! The multi-record text parser Special>Multi-Record Text File Parser does exactly this. Enter tags for the Record ID and for anchor for lines you wish to include in the converted file. Then use the same function in Line Mode to trim the extracted lines.
? I wish to use the LifeTrace program to perform basecalling of my chromatograms. How do I get the software. ! Send me an email and ask. Read the manual to get additional information on the usage of LifeTrace.