I am looking for any reference file that archieves homologous nucleotide sequence (homologous gene) across genome. It could a file harbored in FTP site, a database or a tool for that. Does anyone have any recommendation?
P.S. For clarification, what I would like to get is a list of genes or regions (in human genome) that have similar (homologous) sequences (in human genome). For example, gene ABC1, ABC2 and ABC3 (assuming these are ABC homologs and share similar nucleotide sequence). It would be preferable if I can get a list like this directly. Alternatively, I can use tools such as biopython BLAST E-util or ClustalW to make such list. However, this is a new field to me and I have no idea how should I proceed.
NCBI Homologene, UCSC multi-genome comparisons (example for human, others available, look in pairwise and multiple alignments) and Ensembl Compara.