euGenes/Arthropods About Arthropods EvidentialGene DroSpeGe


Table Ix1.  Homology comparisons of Ixodes scapularis gene sets

  Ixosc19Evigene = Evigene 2019 RNA assembly (3 SRA projects)

  Ixosc14Evigene = Evigene 2014 RNA assembly (1 SRA project)

  Ixosc19NCBI    = NCBI 2019 genome gene models (Ixosc19NCBI) 


a. Ixodes scapularis gene sets aligned to Ixodes ricinis genes

Source          

 Found      

 Best      

Aln% 

pairAln% 

 nConserved 

Ixosc19Evigene  

97%,62619   

91%,58471  

77%

85%

1059/1066

Ixosc14Evigene  

71%,45396   

63%,40933  

76%

81%

1043/1066

Ixosc19NCBI     

52%,33649   

20%,13039  

81%

81%

1030/1066

Reference Ixodes ricinis (Ixoric18TSA) coding sequences, NCBI TSA ID GFVZ01000000, and conserved arthropod genes (BUSCO v9, n=1066).   Ixodes ricinis coding sequences found=64389 among all gene sets, npaired=31879



b. Scorpion proteins x Ixodes tick gene sets

Source           

 Found      

 Best      

Align

Ixosca19Evigene  

99%,20476   

88%,18218  

356

Ixosca19NCBI     

97%,20062   

77%,15977  

351

Ixoric18TSA      

94%,19564   

58%,11968  

304

Reference Centruroides sculpturatus (bark scorpion) of NCBI DEC-2017, GCF_000671375.1_Cexi_2.0;   Scorpion genes found=20736, of total=24591, main isoform



c. Human proteins x Ixodes tick gene sets

Source          

  Found     

  Best     

Align

Ixosca19Evigene 

 98%,14628  

 89%,13283 

396

Ixosca19NCBI    

 97%,14344  

 80%,11890 

391

Ixoric18TSA     

 93%,13785  

 60%,8917  

338

Reference Homo sapiens proteins, NCBI 2018, GCF_000001405.38_GRCh38.p12, Human genes found=14860, of total=20191, main isoform



c. Daphnia proteins x Ixodes tick gene sets

Source          

  Found     

  Best     

 Align

Ixosca19Evigene 

 98%,15096  

 88%,13585 

378

Ixosca19NCBI    

 94%,14393  

 74%,11416 

356

Ixoric18TSA     

 93%,14210  

 59%,9073  

325

Reference Daphnia pulex proteins of EvidentialGene NOV-2017, doi:NNNNN, Daphnia genes found=15351, of total=32989, main isoform


Brief methods: 

   Ix1a. CDS-align with  "blastn -query ref.cds -db test3sets.cds -task dc-megablast -template_type coding",  score best align per test set, count hits/set (Found),   Best/set as any set w/in 1 bp of top match, and average percent aligned to ref CDS.  pairAln% is percent align where both sets matched ref.  Arthropod conserved proteins are measured with Hmmer hmmscan and BUSCO software.

  Ix1b,c,d. Protein align with blastp -query ref.aa -db test3sets.aa,  score best align per test gene set, count hits/set (Found),  Best/set as any set w/in 1 aa of top match, and average align (aa)/set.


Developed at the Genome Informatics Lab of Indiana University Biology Department