[Artemis-users] Problem with /codon_start rendering on -ve strand
Tim et al, I've just run some MAKER2 annotations on a small parasite genome (eukaryotic)., producing a GFF3 file. About 70% of the genes have phase=0 (GFF column 8), while 15% have phase=1 and 15% have phase=2. Artemis seems to load it (mostly) fine, and puts /codon_start=(phase+1) tags. However, when viewing, all the genes look fine on the +strand no matter the phase, but the (some of the?) non-zero phase ones (/codon_start 2 or 3) on the -strand seem to render incorrectly, with the exons being out of frame. I've looked through the mailing list archives, and found one reference to a similar problem, but it appeared to be resolved, but I've reproduced it somehow. I'm using Artemis 14.0.11. I'm also getting possibly related warnings - about 100 x RANGE NOT FOUND ..y. Any help appreciated! -- --Dr Torsten Seemann --Scientific Director : Victorian Bioinformatics Consortium, Monash University, AUSTRALIA --Senior Researcher : VLSCI Life Sciences Computation Centre, Parkville, AUSTRALIA --http://www.bioinformatics.net.au/ ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] BAM in Artemis
Given a BAM file e.g. x.bam the application is looking for the file x.bam.bai in the same directory. It sounds this is the case? If you create the index file with samtools : samtools index x.bam then it will create x.bam.bai. You could try re-creating the index with samtools. I think the .bam file needs to be SORTED too (by reference coordinates) before indexing. Chances are it already is sorted (as it was used with USCS) but just in case: % samtools sort original.bam original-sorted # will create original-sorted.bam % samtools index original-sorted.bam NOTE that for the sort command, you don't put the .bam suffix ... it does it itself (ech). -- --Torsten Seemann --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University, AUSTRALIA ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] Artemis compatibility with BLAST+
Guy, Is there a version of (or suggested edits to) Artemis to make it compatible with NCBI's BLAST+? I edited setup_dbs.sh to deal with makeblastdb replacing formatdb, and that seems to have worked. But it strikes me that any internal calls must use the old blastall command, and I'm not sure how (or even if) that can be addressed ... Or am I better off starting over after downloading the old version of BLAST? Databases created with 'formatdb' (BLAST) can be used by the BLAST+ search tools. A possible work-around for you would be to use the legacy_blast.pl script that comes with BLAST+. It takes the BLAST cmdline options and translates them to a call to BLAST+ tools. If you renamed it blastall with a symlink, it might just work? --Torsten Seemann --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University, AUSTRALIA ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Disable there were warnings while reading message boxes?
Hi all, Is it possible to disable the message box(es) via the command line that say there were warnings while reading - view now? ? If I run art file1.gbk + file2.gff file3.gff I get a warning message box 3 times - 1 per file. It becomes tedious to click No, No, No each time. I understand it is because I am using some non-compliant tags in the 3 files, but I don't want to change the etc/options file to allow them, I just would like to disable the warnings at command line runtime. Is this possible? Any help appreciated, -- --Torsten Seemann --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University, AUSTRALIA ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] Re: Can ACT do a protein comparison?
Peter Tim, what I use for current script using dna for the blast is: seqret -auto -filter -osf fasta $sequence_1 Seq1_fasta seqret -auto -filter -osf fasta $sequence_2 Seq2_fasta formatdb -i Seq1_fasta -p f blastall -d Seq1_fasta -i Seq2_fasta -p tblastx -m 8 -o $outputfile Instead of using 'formatdb' and 'blastall' just to BLAST one sequence against another, I recommend using 'bl2seq' instead - it's a lesser known command which is part of the standard BLAST suite. This removes the need for writing (temporary) database files: seqret -auto -filter -osf fasta $sequence_1 Seq1_fasta seqret -auto -filter -osf fasta $sequence_2 Seq2_fasta bl2seq -i Seq1_fasta -j Seq2_fasta -p tblastx -D 1 The only confusing part is that 'bl2seq' uses the -m parameter for something else, so you need to use -D 1 to do what -m 8 usually does. Most of the other parameters (eg. -e) are the same. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] FW: Tabbed data -
Melanie, Does anyone know a way of taking data for a genome annotated in Artemis and writing out as a table, so for each feature there is a column for /note, /locus_tag, /label, /gene etc. There only seems to be option of writing features out in either Embl or Genbank One thing you may not realise is that MULTIPLE qualifiers of the same name are valid in EMBL/Genbank/DDJB style feature tables. So you will need to consider how you would expect your column-based output to appear in a situation like the one below: FT CDS complement(1..99) FT /product= FT /function= FT /note=no ortholog found FT /note=obvious RBS site FT /EC_number=1.2.3.4 FT /EC_number=2.3.4.5 -- Torsten Seemann Victorian Bioinformatics Consortium, Monash University, Australia http://www.vicbioinformatics.com/ Phone: +61 3 9905 9010 ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] How to integrate hmmpfam in to artemis
How is possible to integrate hmmpfam searches in to artemis in similar way like blast searches (I mean under run menu)? So that you can select ORF and run against pfam database. Yes it is possible. In particular, you would have to write a script called etc/run_hmmpfam, using one of the other run_ scripts as an example. And add 'hmmpfam' item to the 'feature_protein_programs' variable in the etc/options file. You should read http://www.sanger.ac.uk/Software/Artemis/v7/manual/runmenu.html and look in the etc/ directory of Artemis. -- Torsten Seemann [EMAIL PROTECTED] Victorian Bioinformatics Consortium ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Using new EMBL qualifiers
FYI Version 6.4 of the DDBJ/EMBL/GenBank Feature Table is out: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html The CTRL-E editor in Artemis will need to know the new tags: - /experiment and /inference (replacing /evidence) - /rpt_unit_seq and /rpt_unit_range (replacing /rpt_unit) Also, the way Artemis stores its Blast results in /blastp etc perhaps could be augmented with the use of /inference ? Qualifier /inference= Definition a structured description of non-experimental evidence that supports the feature identification or assignment. Value format TYPE[ (same species)][:EVIDENCE_BASIS] Value format TYPE[ (same species)][:EVIDENCE_BASIS] Example /inference=similar to DNA sequence:INSD:AY411252.1 /inference=similar to RNA sequence, mRNA:RefSeq:NM_41.2 /inference=similar to DNA sequence (same species):INSD:AACN010222672.1 /inference=profile:tRNAscan:2.1 /inference=protein motif:InterPro:IPR001900 /inference=ab initio prediction:Genscan:2.0 -- Torsten Seemann [EMAIL PROTECTED] Victorian Bioinformatics Consortium ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
