Converting alignment in image format to text

Question

[Hansen_869]

Hi,

I need the sequences from the attached alignment in text format. However, from the article where the image is from, there is no source of the sequences. I tried image to text converters, but without luck. Any suggestions as to what is the fastest way to retrieve the sequences, without having to search for them one by one using Blast or on Uniprot?

Thanks!

Answer 1

[GenoMax]

Looks like these are UniProt ID's so you should be able to get the sequences from https://www.uniprot.org/uniprotkb?query=CCN*.

You could get individual CCN1* sequences with a specific query: https://www.uniprot.org/uniprotkb?query=CCN1* . Similar for other numbers.

Going down to specific sequences: https://www.uniprot.org/uniprotkb?query=CCN6_DANRE

[Hansen_869]

But I would still manually have to locate the sub-sequence within each sequence right?

[GenoMax]

If you did a multiple sequence alignment then it should be relatively simple to spot the section above.

Asking your favorite AI to convert to text will also lead to something like this which you can refine, that is if f you don't want to do MSA's.

CCN1_PANTR CIVQTTSWSQCSKTCGTGSTRVTNNPECLVKERICEVRPCG
CCN3_BOVINECIEQTTEWSACSKSCGMGSTRVTNNPHCMVKORLCMVRPCD
CCN6_PIG   CLVQATKWTPCSRTCGMGNRITNNSNCNSECMRNERLCYIQP
CCN1_RAT   CIVQTTSWSQCSKSCGTTRVTNLVKEICEVRPG
CCN5_PIG   CPEWSTAWGPCSTTCGLGATRVSNNRFCLETORICEVRPRLCLPGPCP
CCN1_HUMAN CIVQTTSWSOCSKTCGTGSTRVTN NPECLVKEG