Hello all, I have a visualization question and I'm kind of drowning in potential options.
I have the following file for my protein of interest, which I created by manually annotating the file with functional information in Benchling and downloading the gp version. I want to use this information to create an annotated protein alignment with the same protein from other species, to show how various functional domains differ at the amino acid level compared to this species' protein. This can be done in benchling, but I want more control over adding a removing sequences, wrapping text to show the whole protein alignment (it's way to long to show it all linearly) and to isolate different domains to zoom in on. I've been doing this by hand in powerpoint, and there must be a better way. Any open source software (preferably R or Python) that can help with this? Thanks!
LOCUS AT_Protein_Annotated 462 aa linear 14-JUL-2022
DEFINITION .
FEATURES Location/Qualifiers
misc_feature 85..97
/label="Transmembrane Domain"
/color="#f8d3a9"
misc_feature 119..360
/label="VDE"
/color="#b1ff67"
misc_feature 214..221
/label="B1"
/color="#d6b295"
misc_feature 222..232
/label="L1"
/color="#c7b0e3"
misc_feature 227..227
/label="pH"
/color="#f58a5e"
misc_feature 229..233
/label="Dimerization"
/color="#faac61"
misc_feature 230..230
/label="pH"
/color="#f58a5e"
misc_feature 233..239
/label="B2"
/color="#b4abac"
misc_feature 243..253
/label="B3"
/color="#b4abac"
misc_feature 247..253
/label="Dimerization"
/color="#faac61"
misc_feature 251..251
/label="pH"
/color="#f58a5e"
misc_feature 254..258
/label="L3"
/color="#c7b0e3"
misc_feature 259..263
/label="Dimerization"
/color="#faac61"
misc_feature 259..270
/label="B4"
/color="#b4abac"
misc_feature 266..266
/label="Active Site"
/color="#9eafd2"
misc_feature 277..280
/label="B5"
/color="#b4abac"
misc_feature 281..287
/label="L4"
/color="#c7b0e3"
misc_feature 288..288
/label="Active site"
/color="#9eafd2"
misc_feature 288..298
/label="B6"
/color="#b4abac"
misc_feature 290..290
/label="Active site"
/color="#9eafd2"
misc_feature 292..292
/label="Active Site"
/color="#9eafd2"
misc_feature 306..315
/label="B7"
/color="#b4abac"
misc_feature 316..317
/label="L5"
/color="#c7b0e3"
misc_feature 318..328
/label="B8"
/color="#b4abac"
misc_feature 327..327
/label="Active Site"
/color="#9eafd2"
misc_feature 335..347
/label="A1"
/color="#b7e6d7"
misc_feature 352..354
/label="A2"
/color="#b7e6d7"
misc_feature 356..357
/label="B9"
/color="#b4abac"
misc_feature 384..407
/label="Coiled-coil(1)"
/color="#b7e6d7"
misc_feature 416..436
/label="Coiled-coil(2)"
/color="#b7e6d7"
ORIGIN
1 MAVATHCFTS PCHDRIRFFS SDDGIGRLGI TRKRINGTFL LKILPPIQSA DLRTTGGRSS
61 RPLSAFRSGF SKGIFDIVPL PSKNELKELT APLLLKLVGV LACAFLIVPS ADAVDALKTC
121 ACLLKGCRIE LAKCIANPAC AANVACLQTC NNRPDETECQ IKCGDLFENS VVDEFNECAV
181 SRKKCVPRKS DLGEFPAPDP SVLVQNFNIS DFNGKWYITS GLNPTFDAFD CQLHEFHTEG
241 DNKLVGNISW RIKTLDSGFF TRSAVQKFVQ DPNQPGVLYN HDNEYLHYQD DWYILSSKIE
301 NKPEDYIFVY YRGRNDAWDG YGGAVVYTRS SVLPNSIIPE LEKAAKSIGR DFSTFIRTDN
361 TCGPEPALVE RIEKTVEEGE RIIVKEVEEI EEEVEKEVEK VGRTEMTLFQ RLAEGFNELK
421 QDEENFVREL SKEEMEFLDE IKMEASEVEK LFGKALPIRK VR
//
I'm not sure about R or Python. I think you can use MEGA, although I haven't tried it myself. I've used SnapGene in the past, but you would need the full version to perform sequence alignments, which would require a license.