# 
# 09.02.2024
# 
# SynGAP1 amino acid sequence alignments
#
# MAMMAL SIFT INPUT ALIGNMENT
#
# - For performing SIFT predictions using "closely related" mammal species sequences (compare to the animal SIFT below)
# - BLAST search was performed against human SynGAP1 
#  	* UniProt: Human SynGAP1 (Q96PV0 · SYGP1_HUMAN) was searched from the UniProt using BLAST.
# 	* BLAST settings: 
#		* Target database: UniProtKB reference proteomes + Swiss-Prot
#		* Restrict by taxonomy: Mammalia [40674]
#		* Advanced parameters:
#			* Sequence type: Protein
#			* Program: blastp
#			* E-Threshold: 10
#			* Matrix: Auto - BLOSUM62
#			* Filter: None
#			* Gapped: yes
#			* Hits: 1000
#			* HSPs per hit: All
#		* 1000 sequences found with 44.6-100 % identity
#
#	* Advanced Serach: Advanced Search was done to the BLAST results.
#		* Settings: 
#			* Gene Name [GN]: syngap1
#			* OR
#			* Protein Name [DE]: Ras/Rap GTPase-activating protein SynGAP
#			* OR
#			* Protein Name [DE]: Neuronal RasGAP
#			* OR
#			* Protein Name [DE]: Synaptic Ras GTPase-activating protein 1
#			* OR
#			* Protein Name [DE]: Synaptic Ras-GAP 1
#			* NOT
#			* like
#
#	* 440 sequences were found with 44.6-100 % identity and sequences were downloaded in FASTA (canonical) format
#
#	* File: syngap1_uniprot_blast_mammal_sequences_440.fasta
# 
# - Sequence alignment using Schrödinger's MAESTRO version 13.7.125, MMshare Version 6.3.125, Release 2023-3, Platform Linux-x86_64
#
#	* Multiple Sequence Viewer/Editor tool
#	* Settings: MUSCLE Algorithm, Opening gap Penalty 15.00, Extending gap Penalty 1.20
#	* File: maestro_syngap1_mammal_blast_440_alignment_muscle_og_15_eg_1_2.fasta
#
# - Misalinged or non-related parts moved or removed,respectively, from the original alignment
#	* Editing done in MAESTRO manually
#	* File: maestro_syngap1_mammal_blast_440_alignment_muscle_og_15_eg_1_2_edited_final.fasta 
#
##########################################################################################################################################
#
# ANIMAL SIFT INPUT ALIGNMENT
#
# - For performing SIFT predictions using "distantly related" animal species sequences (compare to the mammal SIFT above)
# - BLAST search was performed against human SynGAP1
#  	* UniProt: Human SynGAP1 (Q96PV0 · SYGP1_HUMAN) was searched from the UniProt using BLAST.
# 	* BLAST settings: 
#		* Target database: UniProtKB reference proteomes + Swiss-Prot
#		* Restrict by taxonomy: None
#		* Advanced parameters:
#			* Sequence type: Protein
#			* Program: blastp
#			* E-Threshold: 10
#			* Matrix: Auto - BLOSUM62
#			* Filter: None
#			* Gapped: yes
#			* Hits: 1000
#			* HSPs per hit: All
#	* 1000 sequences were found with 42.8-100 % identity
#
#	* Advanced Serach: Advanced Search was done to the BLAST results.
#		* Settings: 
#			* Gene Name [GN]: syngap1
#			* OR
#			* Protein Name [DE]: Ras/Rap GTPase-activating protein SynGAP
#			* OR
#			* Protein Name [DE]: Neuronal RasGAP
#			* OR
#			* Protein Name [DE]: Synaptic Ras GTPase-activating protein 1
#			* OR
#			* Protein Name [DE]: Synaptic Ras-GAP 1
#			* NOT
#			* like
#
#	* 618 sequences were found with 42.8-100 % identity
#
#	* Sequences with similarity score under 98.8 % were chosen by hand with the Human SynGAP1 sequence
#
#	* 406 sequences were found with similarity score under 98.8 % (Q96PV0 · SYGP1_HUMAN sequence included)
#
# 	* Sequences were added to "My Basket" and they were downloaded in FASTA (canonical) format.
#	
#	* File cleaning: The FASTA file contained human SynGAP1 isoforms 2-4 that had the similarity scores over 98.8 % and rat SynGAP1 isoforms 2, 4 and 5 that had similarity scores over 98.8 %. The isoforms mentioned above were removed from the file.
#
#	* After file cleaning the animal sequence fasta file had 400 sequences
#	* File: syngap1_uniprot_blast_animal_sequences_400_under_989_similarity.fasta
#
# - Sequence alignment using Schrödinger's MAESTRO version 13.7.125, MMshare Version 6.3.125, Release 2023-3, Platform Linux-x86_64
#	* Multiple Sequence Viewer/Editor tool
#	* Settings: MUSCLE Algorithm, Opening gap Penalty 25.00, Extending gap Penalty 3.20
#	* File: maestro_syngap1_uniprot_blast_animal_sequences_400_under_989_similarity_alignment_muscle_og_25_eg_3_2.fasta
#
# - Misalinged or non-related parts moved or removed,respectively, from the original alignment
#	* Editing done in MAESTRO manually
#	* File: maestro_syngap1_uniprot_blast_animal_sequences_400_under_989_similarity_alignment_muscle_og_25_eg_3_2_edited_final.fasta
