ApiDB/EuPathDB Workshop

Intro Survey Results

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  Not Familiar Have Heard of It Slightly Familiar Very Familiar
BLAST 0 (0%) 0 (0%) 6 (22%) 21 (78%)
BLAST X 1 (4%) 3 (11%) 10 (37%) 13 (48%)
BLASTP 1 (4%) 2 (8%) 10 (40%) 12 (48%)
OrthoMCL 10 (37%) 6 (22%) 8 (30%) 3 (11%)
KEGG Map 13 (48%) 6 (22%) 6 (22%) 2 (7%)
PROSITE motif 9 (33%) 7 (26%) 7 (26%) 4 (15%)
PFAM domain 4 (15%) 9 (33%) 6 (22%) 8 (30%)
Signal peptide 2 (7%) 3 (11%) 7 (26%) 15 (56%)
GPI anchor 7 (26%) 1 (4%) 6 (22%) 13 (48%)
HMM 9 (33%) 8 (30%) 7 (26%) 3 (11%)
Transmembrane domain 2 (7%) 3 (11%) 6 (22%) 16 (59%)
Gene 0 (0%) 0 (0%) 0 (0%) 27 (100%)
Contig 0 (0%) 1 (4%) 6 (22%) 20 (74%)
Chromosome 0 (0%) 0 (0%) 1 (4%) 26 (96%)
Daltons 0 (0%) 2 (7%) 2 (7%) 23 (85%)
Annotated 0 (0%) 2 (7%) 6 (22%) 19 (70%)
Curated annotation 4 (15%) 6 (22%) 9 (33%) 8 (30%)
Automated annotation 3 (11%) 5 (19%) 10 (37%) 9 (33%)
Syntenic/Synteny 5 (19%) 11 (41%) 6 (22%) 5 (19%)
EST 1 (4%) 6 (22%) 6 (22%) 14 (52%)
EST Clusters 3 (11%) 8 (30%) 10 (37%) 6 (22%)
EC numbers 7 (26%) 8 (30%) 5 (19%) 7 (26%)
GO term 10 (38%) 7 (27%) 4 (15%) 5 (19%)
CDS 3 (12%) 4 (15%) 2 (8%) 17 (65%)
Translation 0 (0%) 0 (0%) 4 (15%) 23 (85%)
Attributes 6 (22%) 6 (22%) 6 (22%) 9 (33%)
Metabolic Pathway 1 (4%) 3 (11%) 7 (26%) 16 (59%)
Genbank Protein Record 1 (4%) 6 (23%) 9 (35%) 10 (38%)
Genomic context 4 (15%) 5 (19%) 9 (33%) 9 (33%)
GO process 12 (44%) 7 (26%) 2 (7%) 6 (22%)
GO component 14 (52%) 5 (19%) 2 (7%) 6 (22%)
GO function 11 (41%) 8 (30%) 2 (7%) 6 (22%)
GeneDB 5 (19%) 4 (15%) 4 (15%) 14 (52%)
RefSeqs 4 (15%) 10 (38%) 5 (19%) 7 (27%)
CYC Metabolic pathways 16 (62%) 5 (19%) 4 (15%) 1 (4%)
SAGE Tags 10 (37%) 10 (37%) 4 (15%) 3 (11%)
PDB structures 11 (41%) 2 (7%) 10 (37%) 4 (15%)
SignalP 9 (33%) 4 (15%) 7 (26%) 7 (26%)
PlasmoAP 16 (59%) 5 (19%) 6 (22%) 0 (0%)
Mass spec data 2 (7%) 4 (15%) 12 (44%) 9 (33%)
Microarray 0 (0%) 3 (11%) 11 (41%) 13 (48%)
Affymetrix probes 2 (7%) 10 (37%) 8 (30%) 7 (26%)
Affymetrix Genotyped SNP probes 7 (26%) 9 (33%) 9 (33%) 2 (7%)
cDNA microarray 1 (4%) 5 (19%) 10 (37%) 11 (41%)
oligonucleotide microarray 1 (4%) 2 (7%) 13 (48%) 11 (41%)
Pearson Correlation 12 (44%) 8 (30%) 4 (15%) 3 (11%)
Gametocyte 0 (0%) 3 (11%) 9 (33%) 15 (56%)
Non-Redundant Protein DB (NRDB) 4 (15%) 12 (44%) 5 (19%) 6 (22%)
Hydropathy 8 (30%) 8 (30%) 1 (4%) 10 (37%)
Helix 0 (0%) 1 (4%) 7 (26%) 19 (70%)
Coil 1 (4%) 2 (7%) 5 (19%) 19 (70%)
AA sequence 2 (7%) 0 (0%) 3 (11%) 22 (81%)
Promoter 0 (0%) 1 (4%) 5 (19%) 21 (78%)
Centromere 0 (0%) 0 (0%) 8 (30%) 19 (70%)
Oligo 0 (0%) 0 (0%) 5 (19%) 22 (81%)
Sequence Similarity 0 (0%) 0 (0%) 4 (15%) 23 (85%)
cDNA 0 (0%) 1 (4%) 5 (19%) 21 (78%)
ePCR 11 (41%) 7 (26%) 7 (26%) 2 (7%)
Peptide Mass Fingerprinting 6 (22%) 6 (22%) 9 (33%) 6 (22%)
Motif Search 0 (0%) 7 (26%) 9 (33%) 11 (41%)
Mitochondrion 0 (0%) 1 (4%) 4 (15%) 22 (81%)
Apicoplast 1 (4%) 2 (7%) 3 (11%) 21 (78%)
PATS 15 (56%) 9 (33%) 1 (4%) 2 (7%)
ProDom 15 (56%) 5 (19%) 4 (15%) 3 (11%)
Phylogeny 0 (0%) 1 (4%) 5 (19%) 21 (78%)
Protein coding 0 (0%) 0 (0%) 3 (11%) 24 (89%)
Pseudogene 0 (0%) 2 (7%) 9 (33%) 16 (59%)
snRNA 2 (7%) 10 (37%) 6 (22%) 9 (33%)
Telomere 0 (0%) 3 (11%) 4 (15%) 20 (74%)
rRNA 0 (0%) 1 (4%) 2 (7%) 24 (89%)
low complexity 0 (0%) 6 (22%) 12 (44%) 9 (33%)
SNPs 0 (0%) 3 (11%) 15 (56%) 9 (33%)
RefSeq protein 6 (22%) 11 (41%) 2 (7%) 8 (30%)
GenPept protein 10 (37%) 9 (33%) 3 (11%) 5 (19%)
Expression timing 10 (37%) 5 (19%) 6 (22%) 6 (22%)
Expression profile 4 (15%) 3 (11%) 9 (33%) 11 (41%)
Expression level 1 (4%) 2 (8%) 10 (38%) 13 (50%)
Expression profiles correlation 10 (37%) 9 (33%) 6 (22%) 2 (7%)
ncRNA 11 (41%) 9 (33%) 2 (7%) 5 (19%)
Proteomics 0 (0%) 2 (7%) 12 (44%) 13 (48%)
Intergenic region 2 (7%) 5 (19%) 10 (37%) 10 (37%)
UTR 1 (4%) 3 (11%) 9 (33%) 14 (52%)
Ortholog 0 (0%) 5 (19%) 6 (22%) 16 (59%)
Homolog 0 (0%) 2 (7%) 9 (33%) 16 (59%)
Paralog 0 (0%) 7 (27%) 7 (27%) 12 (46%)
Xenolog 13 (50%) 5 (19%) 4 (15%) 4 (15%)
Ortholog Group 2 (8%) 9 (35%) 7 (27%) 8 (31%)
Orthology-based Phylogenetic profile 6 (23%) 6 (23%) 11 (42%) 3 (12%)
PDB structure 7 (27%) 7 (27%) 8 (31%) 4 (15%)
Pubcrawler 13 (50%) 6 (23%) 3 (12%) 4 (15%)
Query 0 (0%) 0 (0%) 7 (27%) 19 (73%)
Boolean 4 (15%) 5 (19%) 8 (31%) 9 (35%)
Join (as in set theory) 15 (58%) 2 (8%) 6 (23%) 3 (12%)
Intersect (as in set theory) 14 (54%) 3 (12%) 6 (23%) 3 (12%)
Subtract (as in set theory) 13 (50%) 4 (15%) 6 (23%) 3 (12%)
Locus 0 (0%) 1 (4%) 9 (35%) 16 (62%)
Wildcard character 6 (23%) 5 (19%) 3 (12%) 12 (46%)
tRNA 0 (0%) 1 (4%) 7 (27%) 18 (69%)
Scaffolds 2 (7%) 5 (19%) 8 (30%) 12 (44%)
SNP density 7 (27%) 7 (27%) 8 (31%) 4 (15%)
Genetic Markers 0 (0%) 4 (15%) 6 (22%) 17 (63%)
Annotation Density 13 (48%) 10 (37%) 3 (11%) 1 (4%)
EST Alignments 4 (15%) 6 (22%) 11 (41%) 6 (22%)
TIGR 2 (7%) 4 (15%) 8 (30%) 13 (48%)
ApiDoTS Alignments 17 (63%) 6 (22%) 4 (15%) 0 (0%)
Unigene 9 (33%) 11 (41%) 3 (11%) 4 (15%)
NCBI 0 (0%) 0 (0%) 6 (22%) 21 (78%)
GLEAN Gene 15 (56%) 7 (26%) 5 (19%) 0 (0%)
TigrScan Gene 7 (26%) 14 (52%) 6 (22%) 0 (0%)
TwinScan Gene Models 12 (46%) 10 (38%) 4 (15%) 0 (0%)
Repeat Regions 0 (0%) 3 (11%) 12 (44%) 12 (44%)
3 -frame translation (reverse) 1 (4%) 4 (15%) 9 (33%) 13 (48%)
3 -frame translation (forward) 1 (4%) 3 (11%) 10 (37%) 13 (48%)
DNA/GC Content 0 (0%) 0 (0%) 4 (15%) 23 (85%)
Genotyped SNPs 2 (7%) 10 (37%) 7 (26%) 8 (30%)
Microsatellite 0 (0%) 4 (15%) 11 (41%) 12 (44%)
Microsatellite map 1 (4%) 8 (30%) 11 (41%) 7 (26%)
GBrowse 2 (7%) 12 (44%) 8 (30%) 5 (19%)
GBrowse track 13 (48%) 7 (26%) 5 (19%) 2 (7%)
Parasite strain 1 (4%) 1 (4%) 3 (11%) 22 (81%)
Parasite isolate 1 (4%) 1 (4%) 3 (11%) 22 (81%)
Allele 0 (0%) 0 (0%) 3 (11%) 24 (89%)
Allele frequency 0 (0%) 2 (7%) 6 (22%) 19 (70%)
Synonymous 0 (0%) 2 (7%) 9 (33%) 16 (59%)
Non-synonmous 0 (0%) 2 (7%) 10 (37%) 15 (56%)
Nonsense 1 (4%) 0 (0%) 6 (22%) 20 (74%)
Dn/Ds 10 (38%) 5 (19%) 7 (27%) 4 (15%)
Interpro 11 (41%) 8 (30%) 5 (19%) 3 (11%)
Epitope 1 (4%) 3 (11%) 5 (19%) 18 (67%)
Isoelectric 1 (4%) 3 (11%) 7 (26%) 16 (59%)
Spectra 2 (7%) 9 (33%) 4 (15%) 12 (44%)
ORF 0 (0%) 0 (0%) 8 (30%) 19 (70%)