There’s a new PhD student in our lab, and I’ve been trying to sort her out with a list of useful tools and websites. I figured that there are probably plenty of other newbies in the field who are fumbling their way around as I did when I started and could benefit from access to my bookmarks bar, so here goes:
When you first start dealing with sequence you may find it useful to know there are tools for converting all sequence types (e.g. FASTA) to RAW format, which is what you’ll need sequence in for lots of alignment softare to use (I genuinely did it by hand a few times before I found that). Also there are obviously tools for reverse transcribing sequence and translating nucleotides into protein sequence.
BLAST (Basic Local Alignment Search Tool) is the ‘search for a gene or a protein’ database that everybody uses across all fields. Use it to find out what an unknown transcript sequence codes for, or how similar it is to the same gene in other species. (Use BLAST-N for nucleotide sequences, BLAST-P for protein to protein, and X for searching for one with the other)
Cereals DB is the wheat-only search engine as maintained by the university of Bristol. Search for 454 genomic sequence (from the University of Liverpool) – e.g. if you’re building a genomic contig to match your cDNA sequence; ESTs – i.e. a summary of where your gene might be expressed or SNPs (although this doesn’t yet tell you which varieties the SNPs are between).
Once you have some sequence, until you get your hands on proper alignment software (this is assuming you’re using <50 sequences – we’re not talking Next Gen data here) like Chromas, DNAman or Sequencher (the latest version does Next Gen but I’m still on 4.10) Clustal W2 is a handy alignment tool. (You’ll need all sequences going in the same direction, so use the reverse transcribe tool above). It works for protein transcripts too.
To find out a bit more about the function of a protein (e.g. what domains it has) use InterPro Scan (which searches other databases like Panther)
For comparative genomics you should be aware of Gramene which allows you to search genomic data for a bunch of plants together. That links to the European Nucleotide Archive, which covers similar ground to the BLAST database and the PlantsDB databases, hosted at MIPS, for if you’re interesting in things other than wheat.
You can get access to the shotgun sequencing data from the IWGSC consortium for particular chromosomes, although you need to request access and get a password. This is useful for mapping your gene of interest.
Has anybody got others that I’ve missed?
Posted in Biology, Genetics, Grad school, Science
Tagged alignment, bioinformatics, BLAST, genetics, genomics, protein, SNPs, wheat
This has been a bad year for farmers: last year’s wet summer and then the cold winter that just won’t end have scuppered one harvest and probably knocked this year’s right down too. Even when conditions are more ideal than they have been this year, farmers and breeders fight an uphill battle trying to prevent a significant proportion of the crop being lost to various pathogens. When it comes to wheat that means rust: black rust, brown rust and yellow rust. Where it strikes, yield losses are likely to be around 20% in susceptible varieties, and the problem is getting much worse. Most resistance to black rust (Puccinia triticina) is caused by a single gene, which a new resistant kind of rust (Ug99) managed to overcome in much the same way as MRSA became resistant to methicillin in our hospitals.
Now scientists from Norwich, Cambridge and the USA are trying to find out how some kinds of a similar disease, yellow rust, (Puccinia striiformis or PST) are able to overcome the plant’s natural defences and infect. Continue reading
Posted in Biology, Genetics, Science
Tagged biology, comparative genomics, genetics, genomics, In the news, microbiology, next gen, pathology, qPCR, rust, science, wheat
When people interested in food security aren’t busy worrying about plateauing crop yields, they tend to be worrying about how much agricultural land we’re losing. We already use so much of the world for growing food crops (around a third) that there’s very little spare land left, and some of the techniques we use for growing crops lead to the land we already have being lost. When crops are grown in an area with insufficient rainfall they must be irrigated (i.e. watered). But all standing water, even if it doesn’t come from the sea, contains small traces of salts: just look at the label on a bottle of Evian. This means that over time, the land becomes saltier or salinised and since plants don’t like salty soil they struggle to grow there. Continue reading
Posted in Biology, Genetics, Science
Tagged biodiversity, biology, crops, DNA, genetics, In the news, IRRI, rice, salinisation, science, scientists, wild relatives
Somehow between going to the Netherlands, the Easter break, a week-long lab course and a conference talk to write I managed to miss not just one, but two really interesting, exciting and useful papers in Nature. (Incidentally, I try not to write too much on here related to my PhD: I’m always a little scared that I’ll end up saying similar things about papers in my literature review and then being pulled up for plagiarism or something, but these are two interesting to miss.) But I digress.
Sequencing the wheat A and D genomes
Two weeks ago a consortium of Chinese and American scientists published two papers about sequencing both the A and the D genome progenitors for bread wheat. (Quick re-cap for the un-initiated. Wheat is a hexaploid i.e. instead of having one maternal and one paternal copy of each chromosome – that is, 2 in total, it has 3 pairs of each, making its genotype AABBDD). This is pretty big news for a couple of reasons: Continue reading
Posted in Biology, Genetics, Molecular Biology 101, Science
Tagged biology, breeding, comparative genomics, conservation, crops, expression, genes, genetic markers, genetics, genomics, In the news, journal, next gen, paper, science, sequencing, wheat
News flash: I have not been having a fun time recently. Well I have: there was Easter for one thing, and a singing competition for another. But there was also one conference before Easter and another one on Wednesday (I just finished my talk: now I’m totally allowed to blog in the middle of the day – right?) and an undergraduate lab course to help run (yes, I know we’re in the middle of vacation: that doesn’t stop 47 unruly undergrads turning up and needing help holding their Gilson the right way up) and somewhere in the middle of it, I got lost. A week of doing some actual exercise (hurrah!), vaguely achieving something at work (double hurrah!) and eating well (whoop!) and I’ve been feeling a bit better.
This weekend was a very rare and special thing: it was a weekend when I had nothing to do. By my standards anyway. I mean, I still had a double gym class, church, a rehearsal and a conference talk to finish, but that’s nothing by my standards. And so I did what any sane person would do on a cold wet April day: I baked a pie.
The great and glorious squash, spinach and goats cheese pie
Posted in Baking
Tagged baking, pastry, pie