Sowing the seeds of bad bioinformatics names

Here are two simple pieces of advice for people who are looking for a name for their latest bioinformatics tool/database/resource:

  1. Avoid common words which might cause people searching for your tool to find something else instead.
  2. Choose a name that hasn't been used before by the bioinformatics community.

Having said that, let's look at a new paper in the journal Bioinformatics:

Seed: a user-friendly tool for exploring and visualizing microbial community data

This name 'Seed', is a not-too-offensive acronym for Simple Exploration of Ecological Data. So what's my beef with it?

The problem is that words like seed are going to appear all over the Internet. My standard test for the 'searchability' of a bioinformatics tool is to search for the tool name followed by the word 'bioinformatics'. Your resource's website or publication should hopefully be the number one result (or somewhere on the first page). However, that is not what happens here.

And searching for 'seed bioinformatics' raises more problems by clashing with my first piece of advice. E.g. here are a couple of papers that were in my first page of Google results:

2010: Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

2011: SEED: efficient clustering of next-generation sequences

So what happens if you include 'microbial' into your search terms? Won't that help?

Nope. Turns out that the SEED — not an ancronym as far as I can tell — is an annotation environment for microbial genomes that has been around for a decade, and which has spawned many papers, e.g.:

2014: The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

All of which means that people looking to find the newly published Seed tool, are not going to have much luck when using search engines.

Is it a 'bad idea' to include gratuitous pictures of cleavage on an Oxford Journals website?

In a word, 'yes'.

2015-02-16: Note that this story has been updated after Oxford Journals contacted me about this (see end of post).

I know that journals need to make money, but it seems a bit shoddy when they allow any form of advertising to appear on their websites. Came across an article at Nucleic Acids Research today which featured the following advert:

Given that I have published in this journal before, I suppose that people reading our articles will also have a chance of seeing ads like this. I would ask Oxford Journals to think carefully about whether they really want adverts like this appearing on their site. This doesn't seem a particularly good fit for them as a scientific publisher — for that matter, it doesn't seem a great fit for for the advertiser either.

Update: Oxford Journals reached out to me on twitter with some good news:

BLAST bug (or feature?) in NCBI BLAST v2.2.30+

Something changed in the latest version of NCBI BLAST+ which breaks our CEGMA software. Compare the behavior of this simple TBLASTN command in v2.2.29+ and v2.2.30+ (from October 2014):

v2.2.29+

tblastn -db sample.dna -query sequence.prot -word_size 5

TBLASTN 2.2.29+

Database: sample.dna
           1 sequences; 2,499,950 total letters

Query= 7292122___KOG0292

Length=1234
                                                 Score     E
Sequences producing significant alignments:      (Bits)  Value

CHROMOSOME_I 1 15072418                           38.9    0.002

v2.2.30+

tblastn -db sample.dna -query sequence.aa -word_size 5

BLAST query/options error: Compressed alphabet lookup table requires word size 6 or 7
Please refer to the BLAST+ user manual.

One step in the CEGMA pipeline involves running TBLASTN with a word size of 5. This no longer works in the latest version and the error message suggests that only a word size of 6 or 7 is permitted. I can confirm that this is the case by looking at the latest source code for the blast_option.c file:


else if (options->lut_type == eCompressedAaLookupTable &&
         options->word_size != 6 && options->word_size != 7) {
         Blast_MessageWrite(blast_msg, eBlastSevError, kBlastMessageNoContext,
               "Compressed alphabet lookup table requires "
               "word size 6 or 7");
         return BLASTERR_OPTION_VALUE_INVALID;
}

The error message suggests I look at the BLAST+ user manual. I did this, and according to Table C5:

tblastn application options:

option = word_size    
type = integer
default value  = 3 
description and notes = "Valid word sizes are 2-7."

There also seems to be no mention of this change in the release notes, all of which makes me think that this is a bug. So I will report this to the NCBI, but any CEGMA users out there may wish to hold off updating to v.2.2.30+.

10 bioinformatics tools you should be using on Valentines Day

1. HUGS: the database of HUman Genome Sequences

"We envisage that the growth in personal genomics will mean that researchers will increasingly want HUGS to cope with their work."


2. LOVE: LncRNA Ortholog Validation and Evaluation

"If you are unsure as to the quality of your lncRNA annotations, we suggest that you need LOVE."


3. KISSES: Kmers In aSsembled SEquenceS 

"We envisage that KISSES will be widely distributed by people working in the field of genome assembly."


4. HEART: Histidine Enrichment Analysis Report Tool

"Accurate detection of histidine-enriched sequences can be achieved if researchers have HEART."


5. ILOVEYOU: Intergenic LOng VariablE Yeast Operational Units

"Detection of this new class of conserved intergenic element will open new avenues for S. cerevisae researchers, and we predict that many will benefit from a deeper understanding of ILOVEYOUs".


6. ROSESARERED: Random Ortholog SEquence Simulations that ARE REDundant

"This tool effectively generates a series of, largely pointless, simulated ortholog sequences. See also our companion software: ValIdation Of Long Eukaryotic TranscriptS thAt Randomly appEar BioLogically UsEful (VIOLETSAREBLUE)."


7. VALENTINE: VALidation of ENcode Transcriptomes IN Eukaryotes

"We believe that the ENCODE annotations of the human genome are only 80% useful, therefore genome annotators will likely appreciate a VALENTINE."

 

8. PASSI(ON): Predicting ASSembly Integrity (Or Not)

"Based on our observations, we feel that there is an urgent need for PASSI(ON) within the genomics community."

 

9. CHOCOLATES: CHOosing COmputationaL AlgoriThms for Testing Evolutionary Simulations

"In a field where which increasingly offers a bewildering choice of bioinformatics tools, we feel that researchers will appreciate CHOCOLATES."


10. SNUGGLES:: SearchiNg for Unique Genes in orGanisms Like Eels and Snakes

"There is a desperate shortage of bioinformatics tools that are dedicated to finding unique genes in creatures that look a bit like worms. Hence we are confident that the community of people who work on snakes, eels, nematodes, and other tubular-like organisms will be receptive to SNUGGLES."