euGenes: Homologous Genes
euGenes .. Fish .. Fly .. Human .. Mouse .. Mosquito .. Rat .. Weed .. Worm .. Yeast Help .. Preferences

euGenes: Homologous Genes Summary Table

Genes with one or more similar genes or homologs in other organisms.
Number and percent with homologs, of total protein sequences available per organism.
  Homologs >
Source		FruitflyHumanMouseWormYeastWeedZebrafishMosquito|AnyN genes
Fruitfly -- 4908
38%		3532
27%		4100
32%		1684
13%		2180
17%		509
3%		0
0%		|5702
44%		12779
Human5485
47%		 -- 7383
63%		4460
38%		1834
15%		2354
20%		1309
11%		0
0%		|8921
76%		11602
Mouse3223
47%		5832
86%		 -- 2631
38%		1003
14%		1300
19%		1024
15%		0
0%		|5989
88%		6757
Worm4550
23%		4365
22%		3236
16%		 -- 1707
8%		2181
11%		510
2%		0
0%		|5315
27%		19228
Yeast1493
24%		1501
24%		1025
16%		1399
22%		 -- 1449
23%		109
1%		0
0%		|1906
30%		6169
Weed3346
14%		3451
14%		2436
10%		3114
13%		2485
10%		 -- 251
1%		0
0%		|4404
18%		23293
Zebrafish440
52%		714
85%		683
82%		316
38%		66
7%		85
10%		 -- 0
0%		|731
87%		831
Mosquito0
0%		0
0%		0
0%		0
0%		0
0%		0
0%		0
0%		 -- |0
0%		0

Genes with one or more similar genes, or paralogs, in same organism.
  FruitflyHumanMouseWormYeastWeedZebrafishMosquito
Paralogs4412
34%		6239
53%		3594
53%		9834
51%		1945
31%		16607
71%		530
63%		0
0%
Source (rows): source protein for BLAST query
Homologs (columns): sequences in BLAST database match with probability <= 1e-30
Any column: Source organism protein have one or more homologs in any organism
N genes column: Number of protein sequences available for the organism

Methods:
This is a computed gene homology or similarity using reference protein sequences identified by the source databases. A BLAST of all these sequences is computed, each sequence against all others, using specific parameters given below.

The sequences used in these calculations are found in the "Reference proteins" data files in each organism's folder. This summary is determined from the "Homologous genes table" data files also in each folder.

You can read the homology summary table best this way. To answer the question what percent of all fruitfly genes have homologs in C.elegans, look at the Fruitfly row, and find the Worm column. To answer the reverse, the Worm row and Fruitfly column says the percent of all worm genes that have fruitfly homologs.

Please note that the summary you find here is based on a specific set of data and homology/similarity (BLAST) calculation parameters. Someone else may publish a different set of values, which would be equally valid, using a different set of data and options for determining "homology". The euGenes summary tries to stay up-to-date by using reference sequences identified by genome databases, and by matching current gene information from these databases with their current sequences.

These values are all moving targets; more data that is coming from genome sequencing projects will change these values. Especially in the euGenes summary, the fruitfly, worm (C.elegans) and yeast data is based on full genome sequences, while man, mouse, weed, and fish are based only on partial sequencing, which may skew values like percent homologies higher than in fact these organisms have.

Asymmetry is due to blast query filter.

Homology computations:
BLAST command: blastall -b 30 -a 4 -e 1e-30 -p blastp -d 'refprot.fa' -i refprot.fa
Matrix=BLOSUM62; Gap Existence=11; Gap Extension=1
No. sequences=82,808; No. letters=37,984,691; Expectation cutoff=1.0e-30
Homologous genes for fish computed 09-July-2001 with BLASTP 2.1.3
Homologous genes for fly computed 09-July-2001 with BLASTP 2.1.3
Homologous genes for man computed 09-July-2001 with BLASTP 2.1.3
Homologous genes for mouse computed 09-July-2001 with BLASTP 2.1.3
Homologous genes for weed computed 09-July-2001 with BLASTP 2.1.3
Homologous genes for worm computed 09-July-2001 with BLASTP 2.1.3
Homologous genes for yeast computed 09-July-2001 with BLASTP 2.1.3

Send comments to us at eugenes@iubio.bio.indiana.edu
euGenes uses Argos: A Replicable Genome infOrmation System