Gene
Gene ID finder:
One known gene ID can be entered and finally get probable IDs in other references.
The Qurey gene ID can be writed in either of the forms, but proper place Helps save time.
At least one check box should be selected. Only one gene ID or FASTA can be entered.
Sequence types are automatically detected.
Protein → blastp
mRNA → blastn
Selection:
All_hit, show all outfmt=6 records from blast, more slower. Default Target number is 10.
Base_align, show all outfmt=0 detail from blastn/blastp, more slower.
Prot_tair give an optimum homologous gene in Arabidopsis thaliana, only runs in blastp mode.
Query_igv give a genome browser iframe, only runs when a geneid provided.
Clicking the aqua blue button in the upper right.
Genome browser: Based on igv.
RefSeq retriever&structer: Download sequence or check gene structure
Pangenome: Blast use 12X Novel sequences.
RNA-seq processor: Include expression and splicing based on V2.4(EnsemblPlants).
ID finder:
Protein
Proteins annotator:
Integrated functionality annotations that rely on diamond blastp and hmmscan.
Alignment depends on the MAFFT and runs after multiple sequences have been submitted.
For annotation-swissprot/tair, only the best one hit preserved when more than one sequence.
Alignment analysis need sequences ≥ 2 and a treefile(iqtree) generated at sequences ≥ 3.
annotator:
SEARCH
Grape V0 id
GSVIVG01000126001
GSVIVT01001909001
JGVv120.1
Vv00s0120g00020
VIT_00024400001
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12X: V2.1: V2.3: V2.4: T2T: T2T.2: (ASM3070453v1) |
LOC117923796 VIT_00s0120g00020 VIT_200s0120g00020 Vitvi17g00617 Vitis01g00007 VitviT2T_002709 |
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Amurensis: Riparia: Trayshed: |
VAG0114172 LOC117923796 hap2.chr10.ver2.0.g380810 |
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Entrez: LOC: RNA: Prot: |
100245777 LOC100233006 XR_002029337.1 XP_010646043.2 |
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At-gene: At-rna: |
AT4G21320 AT4G21320.1 |
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Symbol: Aliases: |
CHS OMT3.1 |
ABC transporter
Genome
Genome tracker:
1. Extract whole or part of contig.
2. Blastn to obtain alignment postion.