Phylogenetic Analyses of IGFBP Family Across 17 Vertebrate and Invertebrate Species

Phylogenetic re-analyses of Insulin-like Growth Factor Binding Proteins (IGFBPs) based on amino acid sequences from 17 species, including human, mouse, anole lizard, coelacanth, and spotted gar. The dataset includes sequence alignments, phylogenetic trees generated via neighbor joining and maximum likelihood methods, and detailed sequence information. It was created by Daniel Ocampo Daza, building upon prior work published in Ocampo Daza et al. (2011).

Use Cases

• Reconstructing evolutionary relationships of IGFBP genes based on the provided amino acid sequence alignment.
• Validating phylogenetic tree construction methods by comparing the neighbor joining and maximum likelihood results included in the dataset.
• Studying protein sequence conservation and variation across diverse species, including fragments from anole lizard, coelacanth, and spotted gar.
• Cross-referencing genomic locations and manual annotations of IGFBP sequences provided in the accompanying spreadsheet.

Strengths

• Includes phylogenetic trees generated by two distinct methods (neighbor joining and maximum likelihood), both supported by bootstrap analyses with 1000 replicates.
• Provides the full amino acid sequence alignment in two standard formats (.aln and .fasta) for direct use in analysis.
• Contains detailed metadata for all sequences in an Excel spreadsheet, including database identifiers, chromosome locations, and manual curation notes.
• Analyses are based on sequences from 17 distinct species, spanning mammals, birds, reptiles, fish, and invertebrates.

Limitations

• Row count and dataset size are unknown, which may limit suitability assessment for large-scale computational tasks.
• Column-level documentation is absent; field semantics for the sequence spreadsheet must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Daniel Ocampo Daza via paperswithcode.

Collection Method

Phylogenetic re-analysis using sequences from genome databases, aligned with ClustalW and edited manually. Trees constructed with ClustalX 2.0 (NJ) and PhyML.