Here you can find a python script I did as part of my MSc in Bioinformatics at UAB.
The script aligns two protein sequences from a Multi-FASTA file using a simplified version of the needleman-wunsch algorithm and reports the score and the alignment in a printable format. The algorithm uses a dynamic programming approach considering that each insertion has a penalty of -4, each deletion has a penalty of -2, and each substitution has a different cost depending on the amino acid substituted using the specified BLOSUM matrix.
The biopython module is required to use the predefined substitution matrices.
Running the following code in a Windows
py -2.7 align.py --input .\\data\\GHRs.fasta --block_size 90
or Linux terminal
python2 align.py --input ./data/GHRs.fasta --block_size 90
will return
Alignment score is: 1165
GHR-II MA--AAL-------------T--LLFCLYILTSSALE--SA--SEQV--H-----PQRDPHLTGCVSANMETFRCRWNVGTLQNLSKPGE 62
|| | || | | || | | | | | | || | | | ||||| | | ||| ||
GHR-I MAVFSSSSSSSSSSSSSSSSTSNLLL-L-LLVSS-LDWLSTRGSVFVMDHMTSSAPV-GPHFTECISREQETFRCWWSPGGFHNLSSPGA 86
GHR-II LRLFYINKLSPLDPPKEWTECPHYS-IDRPNECFFNKNHTSVWTPYKVQLRSRDESTLY-DEN-TFTVDAIVQPDPPVDLTWTTLNESLS 149
|| || | || || ||| || | |||| |||||| || ||| | | || ||| || ||||| | || || | |
GHR-I LRVFYLKKDSP-N--SEWKECPEYSHLKR--ECFFDVNHTSVWIPYCMQLRGQNNVT-YLDEDYCFTVENIVRPDPPVSLNWTLLNISPS 170
GHR-II GTYYDIILSWKPPQSADVAMGWMTLQYEVQY--RSASSDLWHAVE--PVTVTQRSLFGLKHNVNHEVRVRCKMLAG-KEFGEFSDSIF-- 232
| || | || |||| ||| || || | | | | | || || || || | | | ||||||| |
GHR-I GLSYDVMVNWEPPPSADVGAGWMRIEYEIQYTERN-TTN-WEALEMQP-H-TQQTIYGLQIGKEYEVHIRCRMQAFVK-FGEFSDSVFIQ 255
GHR-II V-HIPAKVSSFPV-VALLLFGALCLVAILMLVI-ISQQEKLMFILLPPVPGPKIRGIDPELLKKGKLRELTSIL-GGPPN-LR---PELY 314
| || | || || || | || | | |||| || ||||||| ||| |||||||||||| || || || | | |
GHR-I VTEIPSQDSNFPFKLALI-FGVLGIL-ILILLIGISQQPRLMMILLPPVPAPKIKGIDPELLKKGKLDELNFILSGGGMGGLSTYAPDFY 343
GHR-II NNDPWVEFIDLDIEE-QS-DKLTDL--DTDCLMH--RSLSS--N--CTPVSIGFRDDDSGRASCCDPDLPSDPEASPFHP-LIPNQTLSK 393
|||||| | | | || | | | | | ||||||||| |||| | | | |
GHR-I QDEPWVEFIEVDAEDADAAEKEENQGSDTQRLLDPPQPVSHHMNTGCAN-AVSFPDDDSGRASCYDPDL-HDQDTLMLMATLLPGQPEDG 431
GHR-II EVS--C-QTAS--EPSS-P-VQSPASGEPPFAALGREAMYTQVSEVRSSGKVLLSPEEQTEV-EKTTG-KD-TEKDIM-AE--KEKAKKE 470
| | | | | | || | | | | ||| | || | ||| | | | | | | || ||
GHR-I EDSFDVVERAPVIERSERPLVQTQTGG-PQ-TWLNTD-FYAQVSNVMPSGGVVLSPGQQLRFQESTSAAEDEAQKKGKGSEDSEEKTQKE 518
GHR-II --FQLLVVNADHG-GYTSELNAGKMS-PRLSIGDQSEPGLTG-D-LSPLP-PASPYHESDTTAVSP--LP--P-----APV--YTVVEGV 542
|||||| | ||| | || | | | || | | | | || || | ||| |||| |
GHR-I LQFQLLVVDPE-GSGYTTESNARQISTPP-ST-PM--PG-SGYQTIHPQPVETKPAATAENNQ-SPYILPDSPQSQFFAPVADYTVVQEV 601
GHR-II DRQNSLLLTP--NSTPAPQLII-P-KTMPT-PGGYLTPDLLGSITP 583
| | |||| | | | | | | | || |||||| |
GHR-I DSQHSLLLNPPPRQSPPPCLPHHPTKALAAMPVGYVTPDLLGNLSP 647