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is there a web-based tool to cross-species compare multiple nucleotide or protein sequences for identity and homology in batches

I have a list of 100 50-bp probe sequences that match 100% to respective human genes. I've searched but failed to find any website that allows me to upload the whole 100 sequences and blast them all to, say, mouse genome. Does anyone know if such an online tool exists ? (I am certain code-based tools are available, but unfortunately I am not much a coder - a simple code-based approach is probably okay)

alignment homology
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updated by jared.andrews07 jared.andrews07 • written by CrazyB CrazyB

1 answer

Standard BLAST can do this, you just have to paste or upload your file. You can limit to your organism(s) of interest easily as well.

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written by jared.andrews07 jared.andrews07

There's also the Ensembl BLAST/BLAT page. It defaults to human but you can add/remove species.
Note that for short sequences, you may need to adjust blastn parameters away from default values, e.g. decrease word size and increase e-value.

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written by Jean-Karim Heriche Jean-Karim Heriche

Thanks a lot. Both indeed offer the function for batch sequence comparison !

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written by CrazyB CrazyB

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