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AGRP

Asteraceae Genomic Research Platform

Gene Search

Example:
Example:

Selected Analysis Tools

Bio-informatics Utilities Platform

No. Tool Name Description
1 Blast Call the blast software to perform sequence alignment to arbitrary files.
2 Diamond Call the Diamond software for sequence alignment, arbitrary files.
3 Blast match * Leguminosae sequence alignment and best match.
4 Sequence fetch * Find cds and pep sequences for gene ids.
5 Sequenceserver Leguminosae sequence alignment and Matching visualization.
6 MCScanX Calls MCScanX software to perform collinearity analysis on arbitrary files.
7 ColinearScan Calls the ColinearScan software to perform collinearity analysis on any file.
8 Syntenic visualization A collinear visualization implemented by the invoked Synvisio software based on the results of MCScanX.
9 Dupgen finder The Dupgen finder software is invoked to analyze the type of gene replication.
10 Block number count * Generates the block statistics result based on the ColinearScan result file.
11 ParaAT Call ParaAT to calculate KaKs, generally used to compare pairs of gene sequences, reverse translate and prepare input files.
12 KaKs_Calculator Call KaKs Calculator to calculate KaKs, integrating a variety of algorithms (NG86, YN00, MYN, LWL85, etc.).
13 NG_KaKs_Cal * We calculate kaks using bioperl based on the NEi-Gojobori (NG86) algorithm.
14 B_Dotter * Self-developed blastp dot plot function.
15 BB_Dotter * Self-developed function of drawing block dot plots.
16 BBK_Dotter * Self-developed ks dot plot function.
17 Paleo-gene_identifer * Self-developed Correspondence process to generate the final mc result file.
18 Collinearity generator * Self-developed to generate a collinear list according to multiple mc results generated.
19 Paleo-gene_RI * Self-developed paleo-gene retention statistical tool based on mc results.
20 Paleo-gene_RII * Self-developed ancient gene loss statistical tool based on mc results.
21 P-index-calculator * Self-developed P-index calculation with customizable parameters.
22 Draw_list_trees * Self-developed tree formation based on collinear list.
23 GC-calculation * Calculation of GC content of genome or CDS sequence.
24 Chromosome length extractor * Chromosome length or gene length statistics.
25 Gene_cds_exon_counter * Calculates the length and proportion of cds, exon, intron, and gene in the original gff file.
26 Genome Mount Rate Calculator * Genome mount rate calculator.
27 GF_Circos * Self-developed ks circle diagram function.
28 Codonw Call Codonw, statistical sequence codon situation.
29 Cpgfinder Call Cpgfinder to find CpG islands in the sequence.
30 MEME Suite Motif of invoked memes, predicted proteins.
31 GSDS Called GSDS to achieve the function of drawing gene structure (CDS, UTR, Intron).
32 Hmmer Invoking the Hmmer for gene family screening.
33 Pfam Pfam is invoked to realize the function of identifying protein domains.
34 Interproscan Invoke interproscan software to achieve gene function annotation.
35 Seq alignment Multi-sequence alignment software (mafft, clustalw, and muscle).
36 FastTree Call FastTree software to achieve the function of building a phylogenetic tree.
37 IQ-Tree Call IQ-Tree software to achieve the function of building a phylogenetic tree.
38 TransFam identifier Regulatory protein (RKs) prediction, invoked by iTak software.
39 Heatmap * Calculate correlations between gene expression patterns and metabolite content patterns and draw heat maps.
40 Lollipop * Draw a lollipop chart function for metabolites or gene expression.
41 Gene structure * Function to visualize the position of genes on chromosomes.
42 ShinyCircos Call ShinyCircos to draw a circos diagram.
43 Species classification * Obtain the classification of the species from NCBI in batches.
44 SS-extractor * Extract gene ID information from pep/cds/gff files based on an ID file.
45 SAF-converter * Format conversions including genbank, fasta, embl, fastq, clustal, phylip, and nexus.
46 BDI-finder * Search and replace tool for file contents.
47 BDI-deduplicator * Delete duplicate gene IDs and sequences in pep or cds files.
48 BDI-extractor * Extract data by column from uploaded files.
49 BDI-combiner * File merge tool for multiple files of the same format.
50 Deal_stars * Delete stop codons ("." and "*") from pep protein files.
51 Subtree_extractor * Extracts a specified range of small phylogenetic trees from a large tree file.
52 Block_run Syntenic analysis tool based on WGDI.
53 KaKs calculate Calculation KaKs tool based on WGDI (Nei-Gojobori algorithm/YN00).
54 Blast dotplot WGDI-based blast dotplot tool.
55 Ks dotplot Ks dotplot tool based on WGDI.
56 Block_info Screening out collinear fragments based on WGDI.
57 Correspondence Correspondence process based on WGDI.
58 JBrowse Gene browser function to view genome and GFF files.
59 bbm_extraction Calculation Tool: BLAST Best Match Extractor.
60 ks_distriplot Visualizing Ks Distributions with Seaborn Ridge Plots.
61 cds2geno_dotplot Synteny Visualization based on CDS Mapping.
62 mga_circos Multi-Genome Analysis: Synteny Visualization.